Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/inputs/xbi Working: n-0-138.cluster.ucsf.bkslab.org:/scratch/xiaobo/12845/xbi-8058088.35 Result: /scratch/xiaobo/12845/xbi-8058088.35 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi 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/xbi mkdir: created directory `/scratch/xiaobo/12845' mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35' /scratch/xiaobo/12845/xbi-8058088.35 /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/12845/xbi-8058088.35/working' mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/protonate' Storing results in /scratch/xiaobo/12845/xbi-8058088.35/finished Working in /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 /scratch/xiaobo/12845/xbi-8058088.35/working/protonate /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Using inputs as protomers/tautomers. No processing done 477 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/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Bulk generating 3D conformations all protomers in /scratch/xiaobo/12845/xbi-8058088.35/working/3D mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/12845/xbi-8058088.35/working/protonate/xbi-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 ZINC001458965277 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building' mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001458965277' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001458965277 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC001458965277 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001458965277/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001458965277 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/1 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/1' -> `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/12845/xbi-8058088.35/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: [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, 37, 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: 107 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001458965277 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001458965277 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/finished' Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001458965277/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001458965277 Building ZINC001459029117 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459029117' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459029117 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459029117 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459029117/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459029117 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/2 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2cc(C(F)(F)F)ccc2Cl)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459029117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459029117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459029117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001459029117 none O=C(NCC1(c2cc(C(F)(F)F)ccc2Cl)CC1)[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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 16, 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] 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] 0 hydrogens need rotated 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, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 14, 14, 31, 31, 31, 31, 31, 31, 31, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459029117 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459029117/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459029117 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/3 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/3' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2cc(C(F)(F)F)ccc2Cl)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459029117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459029117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459029117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001459029117 none O=C(NCC1(c2cc(C(F)(F)F)ccc2Cl)CC1)[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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 16, 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] 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] 0 hydrogens need rotated 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, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 14, 14, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459029117 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459029117 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459029117/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459029117/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459029117 Building ZINC001459029117 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459029117' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459029117 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459029117 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459029117/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459029117 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 2) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(NCC1(c2cc(C(F)(F)F)ccc2Cl)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459029117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459029117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459029117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001459029117 none O=C(NCC1(c2cc(C(F)(F)F)ccc2Cl)CC1)[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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 16, 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] 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] 0 hydrogens need rotated 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, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 14, 14, 31, 31, 31, 31, 31, 31, 31, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459029117 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459029117/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459029117 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 3) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(NCC1(c2cc(C(F)(F)F)ccc2Cl)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459029117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459029117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459029117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001459029117 none O=C(NCC1(c2cc(C(F)(F)F)ccc2Cl)CC1)[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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 16, 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] 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] 0 hydrogens need rotated 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, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 14, 14, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459029117 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459029117 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459029117/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459029117/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459029117 Building ZINC001459176079 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176079' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176079 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459176079 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176079/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176079 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/4 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](Cc1ccccc1Br)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001459176079.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459176079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459176079 none CC[C@@H](Cc1ccccc1Br)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 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', 'Br', 'N.am', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 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, 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] 0 hydrogens 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, 5, 13, 21, 21, 13, 21, 21, 21, 2, 3, 1, 2, 1, 1, 1, 6, 6, 2, 6, 10, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 21, 21, 21, 21, 3, 3, 3, 6, 6, 10, 10, 10, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 147 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176079 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176079/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176079 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/5 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/5' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](Cc1ccccc1Br)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001459176079.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459176079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459176079 none CC[C@@H](Cc1ccccc1Br)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 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', 'Br', 'N.am', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 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, 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] 0 hydrogens 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, 4, 11, 17, 17, 11, 17, 17, 17, 2, 2, 1, 2, 1, 1, 1, 6, 6, 2, 6, 14, 6, 6, 6, 5, 5, 5, 5, 5, 11, 11, 17, 17, 16, 17, 2, 2, 2, 6, 6, 14, 14, 14, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 121 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176079 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459176079 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176079/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176079/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176079 Building ZINC001459176079 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176079' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176079 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459176079 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176079/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176079 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 4) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC[C@@H](Cc1ccccc1Br)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001459176079.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459176079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459176079 none CC[C@@H](Cc1ccccc1Br)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 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', 'Br', 'N.am', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 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, 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] 0 hydrogens 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, 5, 13, 21, 21, 13, 21, 21, 21, 2, 3, 1, 2, 1, 1, 1, 6, 6, 2, 6, 10, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 21, 21, 21, 21, 3, 3, 3, 6, 6, 10, 10, 10, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 147 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176079 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176079/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176079 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 5) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC[C@@H](Cc1ccccc1Br)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001459176079.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459176079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176079/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459176079 none CC[C@@H](Cc1ccccc1Br)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 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', 'Br', 'N.am', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 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, 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] 0 hydrogens 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, 4, 11, 17, 17, 11, 17, 17, 17, 2, 2, 1, 2, 1, 1, 1, 6, 6, 2, 6, 14, 6, 6, 6, 5, 5, 5, 5, 5, 11, 11, 17, 17, 16, 17, 2, 2, 2, 6, 6, 14, 14, 14, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 121 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176079 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459176079 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176079/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176079/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176079 Building ZINC001459176083 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176083' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176083 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459176083 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176083/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176083 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/6 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](Cc1ccccc1Br)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001459176083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459176083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459176083 none CC[C@H](Cc1ccccc1Br)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 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', 'Br', 'N.am', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 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, 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] 0 hydrogens 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, 4, 11, 18, 18, 11, 18, 18, 18, 2, 2, 1, 2, 1, 1, 1, 6, 6, 2, 6, 14, 6, 6, 6, 5, 5, 5, 5, 5, 11, 11, 18, 18, 16, 18, 2, 2, 2, 6, 6, 14, 14, 14, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 123 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176083 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176083/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176083 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/7 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/7' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](Cc1ccccc1Br)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001459176083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459176083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459176083 none CC[C@H](Cc1ccccc1Br)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 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', 'Br', 'N.am', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 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, 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] 0 hydrogens 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, 5, 13, 21, 21, 13, 21, 21, 21, 2, 3, 1, 2, 1, 1, 1, 6, 6, 2, 6, 10, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 21, 21, 21, 21, 3, 3, 3, 6, 6, 10, 10, 10, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 147 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176083 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459176083 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176083/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176083/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176083 Building ZINC001459176083 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176083' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176083 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459176083 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176083/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176083 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 6) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC[C@H](Cc1ccccc1Br)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001459176083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459176083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459176083 none CC[C@H](Cc1ccccc1Br)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 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', 'Br', 'N.am', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 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, 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] 0 hydrogens 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, 4, 11, 18, 18, 11, 18, 18, 18, 2, 2, 1, 2, 1, 1, 1, 6, 6, 2, 6, 14, 6, 6, 6, 5, 5, 5, 5, 5, 11, 11, 18, 18, 16, 18, 2, 2, 2, 6, 6, 14, 14, 14, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 123 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176083 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176083/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176083 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 7) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC[C@H](Cc1ccccc1Br)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001459176083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459176083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459176083 none CC[C@H](Cc1ccccc1Br)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 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', 'Br', 'N.am', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 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, 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] 0 hydrogens 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, 5, 13, 21, 21, 13, 21, 21, 21, 2, 3, 1, 2, 1, 1, 1, 6, 6, 2, 6, 10, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 21, 21, 21, 21, 3, 3, 3, 6, 6, 10, 10, 10, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 147 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176083 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459176083 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176083/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176083/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459176083 Building ZINC001459188291 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459188291' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459188291 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459188291 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459188291/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459188291 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/8 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc(F)cc2F)CCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001459188291.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459188291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459188291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001459188291 none O=C(NCC1(c2ccc(F)cc2F)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', 'F', '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, 1, 1, 15, 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: [2, 1, 2, 2, 21, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 7, 7, 7, 7, 7, 2, 13, 13, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 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: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459188291 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459188291/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459188291 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/9 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/9' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc(F)cc2F)CCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001459188291.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459188291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459188291/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001459188291 none O=C(NCC1(c2ccc(F)cc2F)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', 'F', '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, 1, 1, 15, 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, 19, 34, 35, 35, 34, 35, 35, 35, 35, 34, 34, 34, 34, 1, 1, 1, 6, 6, 6, 6, 6, 3, 13, 13, 35, 35, 35, 34, 34, 34, 34, 34, 34, 34, 34, 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]) total number of confs: 110 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459188291 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459188291 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459188291/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459188291/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459188291 Building ZINC001459188291 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459188291' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459188291 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459188291 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459188291/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459188291 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 8) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(NCC1(c2ccc(F)cc2F)CCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001459188291.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459188291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459188291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001459188291 none O=C(NCC1(c2ccc(F)cc2F)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', 'F', '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, 1, 1, 15, 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: [2, 1, 2, 2, 21, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 7, 7, 7, 7, 7, 2, 13, 13, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 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: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459188291 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459188291/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459188291 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 9) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(NCC1(c2ccc(F)cc2F)CCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001459188291.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459188291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459188291/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001459188291 none O=C(NCC1(c2ccc(F)cc2F)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', 'F', '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, 1, 1, 15, 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, 19, 34, 35, 35, 34, 35, 35, 35, 35, 34, 34, 34, 34, 1, 1, 1, 6, 6, 6, 6, 6, 3, 13, 13, 35, 35, 35, 34, 34, 34, 34, 34, 34, 34, 34, 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]) total number of confs: 110 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459188291 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459188291 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459188291/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459188291/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459188291 Building ZINC001459225294 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225294' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225294 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459225294 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225294/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225294 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/10 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccn1)c1ccc(Br)cc1) `ZINC001459225294.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459225294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001459225294 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccn1)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 9, 9, 26, 46, 46, 46, 46, 46, 9, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 4, 26, 26, 46, 46, 46, 46, 15, 15, 15, 15] 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: 159 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225294 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225294/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225294 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/11 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/11' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccn1)c1ccc(Br)cc1) `ZINC001459225294.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459225294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225294/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001459225294 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccn1)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 8, 8, 27, 47, 47, 47, 47, 47, 8, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 4, 27, 27, 47, 47, 47, 47, 15, 15, 15, 15] 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: 167 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225294 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459225294 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225294/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225294/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225294 Building ZINC001459225294 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225294' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225294 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459225294 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225294/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225294 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 10) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccn1)c1ccc(Br)cc1) `ZINC001459225294.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459225294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001459225294 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccn1)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 9, 9, 26, 46, 46, 46, 46, 46, 9, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 4, 26, 26, 46, 46, 46, 46, 15, 15, 15, 15] 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: 159 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225294 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225294/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225294 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 11) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccn1)c1ccc(Br)cc1) `ZINC001459225294.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459225294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225294/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001459225294 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1ccccn1)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 8, 8, 27, 47, 47, 47, 47, 47, 8, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 3, 3, 4, 27, 27, 47, 47, 47, 47, 15, 15, 15, 15] 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: 167 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225294 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459225294 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225294/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225294/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225294 Building ZINC001459225299 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225299' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225299 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459225299 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225299/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225299 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/12 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](Cc1ccccn1)c1ccc(Br)cc1) `ZINC001459225299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459225299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001459225299 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](Cc1ccccn1)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 8, 8, 27, 47, 47, 47, 47, 47, 8, 15, 15, 13, 15, 15, 15, 3, 3, 3, 3, 3, 3, 4, 27, 27, 47, 47, 47, 47, 15, 15, 15, 15] 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: 177 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225299 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225299/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225299 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/13 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/13' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H](Cc1ccccn1)c1ccc(Br)cc1) `ZINC001459225299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459225299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001459225299 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H](Cc1ccccn1)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 9, 9, 26, 46, 46, 46, 46, 46, 9, 15, 15, 12, 15, 15, 15, 3, 3, 3, 3, 3, 3, 4, 26, 26, 46, 46, 46, 46, 15, 15, 15, 15] 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: 174 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225299 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459225299 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225299/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225299/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225299 Building ZINC001459225299 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225299' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225299 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459225299 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225299/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225299 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 12) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](Cc1ccccn1)c1ccc(Br)cc1) `ZINC001459225299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459225299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001459225299 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](Cc1ccccn1)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 8, 8, 27, 47, 47, 47, 47, 47, 8, 15, 15, 13, 15, 15, 15, 3, 3, 3, 3, 3, 3, 4, 27, 27, 47, 47, 47, 47, 15, 15, 15, 15] 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: 177 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225299 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225299/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225299 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 13) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H](Cc1ccccn1)c1ccc(Br)cc1) `ZINC001459225299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459225299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001459225299 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H](Cc1ccccn1)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 9, 9, 26, 46, 46, 46, 46, 46, 9, 15, 15, 12, 15, 15, 15, 3, 3, 3, 3, 3, 3, 4, 26, 26, 46, 46, 46, 46, 15, 15, 15, 15] 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: 174 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225299 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459225299 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225299/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225299/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459225299 Building ZINC001459318984 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459318984' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459318984 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459318984 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459318984/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459318984 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/14 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/14' -> `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)Nc1ccnc(OC(C)C)c1) `ZINC001459318984.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459318984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459318984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001459318984 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccnc(OC(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.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'] dock atom 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, 1, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 12, 16, 16, 7, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 2, 7, 7, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 78 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459318984 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459318984/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459318984 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/15 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/15' -> `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)Nc1ccnc(OC(C)C)c1) `ZINC001459318984.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459318984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459318984/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001459318984 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccnc(OC(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.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'] dock atom 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, 1, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 12, 14, 14, 8, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 8, 8, 14, 14, 14, 14, 14, 14, 14, 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: 62 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459318984 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459318984 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459318984/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459318984/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459318984 Building ZINC001459318984 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459318984' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459318984 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459318984 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459318984/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459318984 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 14) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccnc(OC(C)C)c1) `ZINC001459318984.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459318984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459318984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001459318984 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccnc(OC(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.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'] dock atom 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, 1, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 12, 16, 16, 7, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 2, 7, 7, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 78 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459318984 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459318984/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459318984 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 15) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccnc(OC(C)C)c1) `ZINC001459318984.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459318984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459318984/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001459318984 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccnc(OC(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.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'] dock atom 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, 1, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 12, 14, 14, 8, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 8, 8, 14, 14, 14, 14, 14, 14, 14, 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: 62 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459318984 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459318984 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459318984/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459318984/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459318984 Building ZINC001459368586 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459368586' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459368586 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459368586 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459368586/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459368586 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/16 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccncc2)c2ccc(F)c(Br)c2)c1) `ZINC001459368586.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459368586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459368586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001459368586 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccncc2)c2ccc(F)c(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', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 15, 1, 17, 1, 1, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 5, 5, 1, 1, 1, 1, 4, 4, 5, 11, 15, 15, 15, 15, 15, 5, 16, 16, 8, 16, 16, 16, 16, 5, 5, 5, 5, 2, 5, 5, 11, 11, 15, 15, 15, 15, 16, 16, 16, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459368586 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459368586/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459368586 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/17 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/17' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N(Cc2ccncc2)c2ccc(F)c(Br)c2)c1) `ZINC001459368586.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459368586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459368586/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001459368586 none Cc1cccc([C@]([O-])([SiH3])C(=O)N(Cc2ccncc2)c2ccc(F)c(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', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 15, 1, 17, 1, 1, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 5, 5, 1, 1, 1, 1, 4, 4, 5, 10, 14, 14, 14, 14, 14, 5, 17, 17, 9, 17, 17, 17, 17, 5, 5, 5, 5, 2, 5, 5, 10, 10, 14, 14, 14, 14, 17, 17, 17, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459368586 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459368586 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459368586/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459368586/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459368586 Building ZINC001459368586 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459368586' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459368586 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459368586 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459368586/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459368586 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 16) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccncc2)c2ccc(F)c(Br)c2)c1) `ZINC001459368586.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459368586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459368586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001459368586 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N(Cc2ccncc2)c2ccc(F)c(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', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 15, 1, 17, 1, 1, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 5, 5, 1, 1, 1, 1, 4, 4, 5, 11, 15, 15, 15, 15, 15, 5, 16, 16, 8, 16, 16, 16, 16, 5, 5, 5, 5, 2, 5, 5, 11, 11, 15, 15, 15, 15, 16, 16, 16, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459368586 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459368586/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459368586 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 17) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N(Cc2ccncc2)c2ccc(F)c(Br)c2)c1) `ZINC001459368586.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459368586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459368586/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001459368586 none Cc1cccc([C@]([O-])([SiH3])C(=O)N(Cc2ccncc2)c2ccc(F)c(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', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 15, 1, 17, 1, 1, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 5, 5, 1, 1, 1, 1, 4, 4, 5, 10, 14, 14, 14, 14, 14, 5, 17, 17, 9, 17, 17, 17, 17, 5, 5, 5, 5, 2, 5, 5, 10, 10, 14, 14, 14, 14, 17, 17, 17, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459368586 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459368586 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459368586/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459368586/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459368586 Building ZINC001459455933 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459455933' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459455933 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459455933 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459455933/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459455933 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/18 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1c1ncc2n1CCCC2)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001459455933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459455933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459455933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459455933 none O=C(Nc1ccccc1c1ncc2n1CCCC2)[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.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 1, 1, 1, 1, 8, 1, 1, 8, 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, 7, 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, 1, 6, 6, 14, 14, 14, 14, 14, 14, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 10, 10, 10, 10, 10, 6, 14, 14, 14, 14, 29, 29, 29, 29, 29, 29, 29, 29, 29, 10, 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459455933 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459455933/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459455933 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/19 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/19' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1c1ncc2n1CCCC2)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001459455933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459455933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459455933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459455933 none O=C(Nc1ccccc1c1ncc2n1CCCC2)[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.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 1, 1, 1, 1, 8, 1, 1, 8, 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, 7, 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, 5, 13, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 10, 10, 10, 10, 10, 5, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459455933 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459455933 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459455933/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459455933/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459455933 Building ZINC001459455933 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459455933' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459455933 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459455933 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459455933/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459455933 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 18) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ccccc1c1ncc2n1CCCC2)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001459455933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459455933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459455933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459455933 none O=C(Nc1ccccc1c1ncc2n1CCCC2)[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.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 1, 1, 1, 1, 8, 1, 1, 8, 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, 7, 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, 1, 6, 6, 14, 14, 14, 14, 14, 14, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 10, 10, 10, 10, 10, 6, 14, 14, 14, 14, 29, 29, 29, 29, 29, 29, 29, 29, 29, 10, 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459455933 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459455933/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459455933 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 19) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ccccc1c1ncc2n1CCCC2)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001459455933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459455933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459455933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459455933 none O=C(Nc1ccccc1c1ncc2n1CCCC2)[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.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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, 1, 1, 1, 1, 8, 1, 1, 8, 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, 7, 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, 5, 13, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 10, 10, 10, 10, 10, 5, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459455933 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459455933 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459455933/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459455933/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459455933 Building ZINC001459513133 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459513133' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459513133 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459513133 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459513133/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459513133 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/20 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3cccc(Br)c3)CC2)cc1Cl) `ZINC001459513133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459513133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459513133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001459513133 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3cccc(Br)c3)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', 'Br', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 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: [5, 3, 3, 3, 3, 1, 1, 1, 1, 4, 5, 7, 7, 7, 7, 27, 27, 12, 27, 27, 27, 7, 7, 3, 3, 3, 5, 5, 5, 3, 3, 7, 7, 7, 7, 7, 27, 27, 17, 27, 7, 7, 7, 7, 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: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459513133 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459513133/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459513133 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/21 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/21' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3cccc(Br)c3)CC2)cc1Cl) `ZINC001459513133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459513133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459513133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001459513133 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3cccc(Br)c3)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', 'Br', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 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: [6, 4, 2, 4, 4, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 25, 25, 9, 25, 25, 25, 5, 5, 4, 4, 4, 6, 6, 6, 4, 4, 5, 5, 5, 5, 5, 25, 25, 17, 25, 5, 5, 5, 5, 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459513133 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459513133 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459513133/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459513133/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459513133 Building ZINC001459513133 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459513133' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459513133 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459513133 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459513133/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459513133 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 20) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3cccc(Br)c3)CC2)cc1Cl) `ZINC001459513133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459513133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459513133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001459513133 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3cccc(Br)c3)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', 'Br', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 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: [5, 3, 3, 3, 3, 1, 1, 1, 1, 4, 5, 7, 7, 7, 7, 27, 27, 12, 27, 27, 27, 7, 7, 3, 3, 3, 5, 5, 5, 3, 3, 7, 7, 7, 7, 7, 27, 27, 17, 27, 7, 7, 7, 7, 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: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459513133 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459513133/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459513133 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 21) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3cccc(Br)c3)CC2)cc1Cl) `ZINC001459513133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459513133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459513133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001459513133 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3cccc(Br)c3)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', 'Br', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 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: [6, 4, 2, 4, 4, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 25, 25, 9, 25, 25, 25, 5, 5, 4, 4, 4, 6, 6, 6, 4, 4, 5, 5, 5, 5, 5, 25, 25, 17, 25, 5, 5, 5, 5, 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459513133 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459513133 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459513133/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459513133/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459513133 Building ZINC001459516850 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459516850' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459516850 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459516850 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459516850/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459516850 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/22 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2ccc(C)c(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)c2)cn1) `ZINC001459516850.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459516850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459516850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459516850 none COc1ccc(c2ccc(C)c(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)c2)cn1 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', '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', 'N.ar', 'H', '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, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 8, 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, 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] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 8, 28, 28, 28, 28, 28, 28, 28, 8, 8, 8, 8, 8, 3, 7, 7, 8, 28] 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]) total number of confs: 49 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459516850 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459516850/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459516850 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/23 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/23' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2ccc(C)c(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)c2)cn1) `ZINC001459516850.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459516850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459516850/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459516850 none COc1ccc(c2ccc(C)c(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)c2)cn1 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', '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', 'N.ar', 'H', '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, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 8, 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, 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] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 28, 28, 28, 28, 28, 28, 28, 8, 8, 8, 8, 8, 3, 8, 8, 8, 28] 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]) total number of confs: 50 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459516850 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459516850 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459516850/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459516850/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459516850 Building ZINC001459516850 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459516850' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459516850 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459516850 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459516850/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459516850 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 22) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc(c2ccc(C)c(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)c2)cn1) `ZINC001459516850.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459516850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459516850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459516850 none COc1ccc(c2ccc(C)c(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)c2)cn1 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', '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', 'N.ar', 'H', '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, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 8, 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, 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] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 8, 28, 28, 28, 28, 28, 28, 28, 8, 8, 8, 8, 8, 3, 7, 7, 8, 28] 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]) total number of confs: 49 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459516850 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459516850/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459516850 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 23) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc(c2ccc(C)c(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)c2)cn1) `ZINC001459516850.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459516850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459516850/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459516850 none COc1ccc(c2ccc(C)c(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)c2)cn1 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', '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', 'N.ar', 'H', '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, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 8, 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, 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] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 28, 28, 28, 28, 28, 28, 28, 8, 8, 8, 8, 8, 3, 8, 8, 8, 28] 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]) total number of confs: 50 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459516850 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459516850 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459516850/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459516850/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459516850 Building ZINC001459597910 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001459597910 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/24 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H]1CC[N@](c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001459597910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459597910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459597910 none CN(C)C[C@H]1CC[N@](c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)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', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 34, 34, 34, 34, 34, 10, 8, 8, 6, 8, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 34, 34, 44, 44, 44, 44, 44, 44, 44, 44, 34, 34, 34, 34, 8, 8, 8, 8, 3, 3, 1, 3, 34, 34, 34, 34] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/25 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/25' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H]1CC[N@@](c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001459597910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459597910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459597910 none CN(C)C[C@H]1CC[N@@](c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)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', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 34, 34, 34, 34, 34, 11, 9, 9, 6, 9, 9, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 34, 34, 44, 44, 44, 44, 44, 44, 44, 44, 34, 34, 34, 34, 9, 9, 9, 9, 3, 3, 1, 3, 34, 34, 34, 34] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/26 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/26' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H]1CC[N@](c2ccccc2NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001459597910.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001459597910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459597910 none CN(C)C[C@H]1CC[N@](c2ccccc2NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)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', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 31, 31, 31, 31, 31, 11, 9, 9, 6, 9, 9, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 31, 31, 44, 44, 44, 44, 44, 44, 44, 44, 31, 31, 31, 31, 9, 9, 9, 9, 4, 3, 1, 3, 31, 31, 31, 31] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/27 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/27' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H]1CC[N@@](c2ccccc2NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001459597910.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001459597910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459597910 none CN(C)C[C@H]1CC[N@@](c2ccccc2NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)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', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 32, 32, 11, 9, 9, 6, 9, 9, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 32, 32, 45, 45, 45, 45, 45, 45, 45, 45, 32, 32, 32, 32, 9, 9, 9, 9, 4, 3, 1, 3, 32, 32, 32, 32] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459597910 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 Building ZINC001459597910 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001459597910 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 24) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CN(C)C[C@H]1CC[N@](c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001459597910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459597910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459597910 none CN(C)C[C@H]1CC[N@](c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)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', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 34, 34, 34, 34, 34, 10, 8, 8, 6, 8, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 34, 34, 44, 44, 44, 44, 44, 44, 44, 44, 34, 34, 34, 34, 8, 8, 8, 8, 3, 3, 1, 3, 34, 34, 34, 34] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 25) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CN(C)C[C@H]1CC[N@@](c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001459597910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459597910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459597910 none CN(C)C[C@H]1CC[N@@](c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)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', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 34, 34, 34, 34, 34, 11, 9, 9, 6, 9, 9, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 34, 34, 44, 44, 44, 44, 44, 44, 44, 44, 34, 34, 34, 34, 9, 9, 9, 9, 3, 3, 1, 3, 34, 34, 34, 34] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 26) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/26: 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@](c2ccccc2NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001459597910.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001459597910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459597910 none CN(C)C[C@H]1CC[N@](c2ccccc2NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)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', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 31, 31, 31, 31, 31, 11, 9, 9, 6, 9, 9, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 31, 31, 44, 44, 44, 44, 44, 44, 44, 44, 31, 31, 31, 31, 9, 9, 9, 9, 4, 3, 1, 3, 31, 31, 31, 31] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 27) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/27: 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@@](c2ccccc2NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001459597910.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001459597910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459597910 none CN(C)C[C@H]1CC[N@@](c2ccccc2NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)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', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 32, 32, 11, 9, 9, 6, 9, 9, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 32, 32, 45, 45, 45, 45, 45, 45, 45, 45, 32, 32, 32, 32, 9, 9, 9, 9, 4, 3, 1, 3, 32, 32, 32, 32] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459597910 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 Building ZINC001459597910 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001459597910 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 24) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CN(C)C[C@H]1CC[N@](c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001459597910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459597910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459597910 none CN(C)C[C@H]1CC[N@](c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)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', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 34, 34, 34, 34, 34, 10, 8, 8, 6, 8, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 34, 34, 44, 44, 44, 44, 44, 44, 44, 44, 34, 34, 34, 34, 8, 8, 8, 8, 3, 3, 1, 3, 34, 34, 34, 34] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 25) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CN(C)C[C@H]1CC[N@@](c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001459597910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459597910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459597910 none CN(C)C[C@H]1CC[N@@](c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)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', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 34, 34, 34, 34, 34, 11, 9, 9, 6, 9, 9, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 34, 34, 44, 44, 44, 44, 44, 44, 44, 44, 34, 34, 34, 34, 9, 9, 9, 9, 3, 3, 1, 3, 34, 34, 34, 34] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 26) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/26: 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@](c2ccccc2NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001459597910.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001459597910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459597910 none CN(C)C[C@H]1CC[N@](c2ccccc2NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)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', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 31, 31, 31, 31, 31, 11, 9, 9, 6, 9, 9, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 31, 31, 44, 44, 44, 44, 44, 44, 44, 44, 31, 31, 31, 31, 9, 9, 9, 9, 4, 3, 1, 3, 31, 31, 31, 31] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 27) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/27: 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@@](c2ccccc2NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001459597910.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001459597910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459597910 none CN(C)C[C@H]1CC[N@@](c2ccccc2NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)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', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 32, 32, 11, 9, 9, 6, 9, 9, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 32, 32, 45, 45, 45, 45, 45, 45, 45, 45, 32, 32, 32, 32, 9, 9, 9, 9, 4, 3, 1, 3, 32, 32, 32, 32] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459597910 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 Building ZINC001459597910 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001459597910 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 24) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CN(C)C[C@H]1CC[N@](c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001459597910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459597910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459597910 none CN(C)C[C@H]1CC[N@](c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)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', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 34, 34, 34, 34, 34, 10, 8, 8, 6, 8, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 34, 34, 44, 44, 44, 44, 44, 44, 44, 44, 34, 34, 34, 34, 8, 8, 8, 8, 3, 3, 1, 3, 34, 34, 34, 34] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 25) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CN(C)C[C@H]1CC[N@@](c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001459597910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459597910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459597910 none CN(C)C[C@H]1CC[N@@](c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)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', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 34, 34, 34, 34, 34, 11, 9, 9, 6, 9, 9, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 34, 34, 44, 44, 44, 44, 44, 44, 44, 44, 34, 34, 34, 34, 9, 9, 9, 9, 3, 3, 1, 3, 34, 34, 34, 34] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 26) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/26: 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@](c2ccccc2NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001459597910.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001459597910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459597910 none CN(C)C[C@H]1CC[N@](c2ccccc2NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)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', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 31, 31, 31, 31, 31, 11, 9, 9, 6, 9, 9, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 31, 31, 44, 44, 44, 44, 44, 44, 44, 44, 31, 31, 31, 31, 9, 9, 9, 9, 4, 3, 1, 3, 31, 31, 31, 31] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 27) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/27: 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@@](c2ccccc2NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001459597910.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001459597910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459597910 none CN(C)C[C@H]1CC[N@@](c2ccccc2NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)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', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 32, 32, 11, 9, 9, 6, 9, 9, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 32, 32, 45, 45, 45, 45, 45, 45, 45, 45, 32, 32, 32, 32, 9, 9, 9, 9, 4, 3, 1, 3, 32, 32, 32, 32] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459597910 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459597910 Building ZINC001459703392 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459703392' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459703392 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459703392 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459703392/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459703392 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/28 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3oc(SCc4ccccc4)nc3c2)cn1) `ZINC001459703392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459703392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459703392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459703392 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3oc(SCc4ccccc4)nc3c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 1, 1, 1, 1, 12, 1, 14, 5, 1, 1, 1, 1, 1, 1, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 27, 40, 40, 40, 40, 40, 40, 8, 8, 8, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 8, 8, 40, 40, 40, 40, 40, 40, 40, 8, 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459703392 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459703392/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459703392 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 29) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/29 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/29' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3oc(SCc4ccccc4)nc3c2)cn1) `ZINC001459703392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459703392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459703392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459703392 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3oc(SCc4ccccc4)nc3c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 1, 1, 1, 1, 12, 1, 14, 5, 1, 1, 1, 1, 1, 1, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 27, 39, 39, 39, 39, 39, 39, 8, 8, 8, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 8, 8, 39, 39, 39, 39, 39, 39, 39, 8, 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459703392 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459703392 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459703392/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459703392/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459703392 Building ZINC001459703392 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459703392' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459703392 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459703392 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459703392/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459703392 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 28) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3oc(SCc4ccccc4)nc3c2)cn1) `ZINC001459703392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459703392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459703392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459703392 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3oc(SCc4ccccc4)nc3c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 1, 1, 1, 1, 12, 1, 14, 5, 1, 1, 1, 1, 1, 1, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 27, 40, 40, 40, 40, 40, 40, 8, 8, 8, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 8, 8, 40, 40, 40, 40, 40, 40, 40, 8, 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459703392 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459703392/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459703392 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 29) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3oc(SCc4ccccc4)nc3c2)cn1) `ZINC001459703392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459703392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459703392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459703392 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3oc(SCc4ccccc4)nc3c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 1, 1, 1, 1, 12, 1, 14, 5, 1, 1, 1, 1, 1, 1, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 27, 39, 39, 39, 39, 39, 39, 8, 8, 8, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 8, 8, 39, 39, 39, 39, 39, 39, 39, 8, 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459703392 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459703392 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459703392/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459703392/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459703392 Building ZINC001459779890 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459779890' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459779890 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459779890 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459779890/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459779890 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/30 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/30' -> `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(Br)c(F)cc1C) `ZINC001459779890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459779890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459779890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001459779890 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Br)c(F)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.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 17, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 4, 15, 15, 4, 4, 1, 1, 1, 1, 6, 6, 6, 30, 30, 30, 15, 30, 30, 30, 30, 4, 4, 4, 15, 15, 6, 15, 15, 4, 4, 4, 6, 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]) total number of confs: 139 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459779890 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459779890/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459779890 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 31) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/31 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/31' -> `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(Br)c(F)cc1C) `ZINC001459779890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459779890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459779890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001459779890 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Br)c(F)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.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 17, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 4, 15, 15, 4, 4, 1, 1, 1, 1, 6, 6, 6, 30, 30, 30, 15, 30, 30, 30, 30, 4, 4, 4, 15, 15, 4, 15, 15, 4, 4, 4, 6, 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]) total number of confs: 132 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459779890 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459779890 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459779890/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459779890/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459779890 Building ZINC001459779890 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459779890' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459779890 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459779890 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459779890/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459779890 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 30) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Br)c(F)cc1C) `ZINC001459779890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459779890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459779890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001459779890 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Br)c(F)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.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 17, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 4, 15, 15, 4, 4, 1, 1, 1, 1, 6, 6, 6, 30, 30, 30, 15, 30, 30, 30, 30, 4, 4, 4, 15, 15, 6, 15, 15, 4, 4, 4, 6, 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]) total number of confs: 139 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459779890 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459779890/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459779890 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 31) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Br)c(F)cc1C) `ZINC001459779890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459779890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459779890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001459779890 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Br)c(F)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.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 17, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 4, 15, 15, 4, 4, 1, 1, 1, 1, 6, 6, 6, 30, 30, 30, 15, 30, 30, 30, 30, 4, 4, 4, 15, 15, 4, 15, 15, 4, 4, 4, 6, 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]) total number of confs: 132 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459779890 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459779890 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459779890/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459779890/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459779890 Building ZINC001459801531 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459801531' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459801531 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459801531 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459801531/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459801531 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/32 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/32' -> `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)c1ccc(OC(F)(F)F)cc1) `ZINC001459801531.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459801531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459801531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001459801531 none CC(C)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(OC(F)(F)F)cc1 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', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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, 12, 5, 15, 15, 15, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 12, 5, 10, 41, 41, 41, 41, 12, 12, 5, 5, 5, 5, 5, 5, 3, 5, 5, 12, 12, 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459801531 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459801531/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459801531 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 33) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/33 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/33' -> `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)c1ccc(OC(F)(F)F)cc1) `ZINC001459801531.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459801531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459801531/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001459801531 none CC(C)(NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(OC(F)(F)F)cc1 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', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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, 12, 5, 15, 15, 15, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 12, 5, 10, 42, 42, 42, 42, 12, 12, 5, 5, 5, 5, 5, 5, 3, 5, 5, 12, 12, 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459801531 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459801531 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459801531/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459801531/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459801531 Building ZINC001459801531 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459801531' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459801531 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459801531 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459801531/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459801531 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 32) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(OC(F)(F)F)cc1) `ZINC001459801531.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459801531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459801531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001459801531 none CC(C)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(OC(F)(F)F)cc1 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', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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, 12, 5, 15, 15, 15, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 12, 5, 10, 41, 41, 41, 41, 12, 12, 5, 5, 5, 5, 5, 5, 3, 5, 5, 12, 12, 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459801531 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459801531/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459801531 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 33) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(OC(F)(F)F)cc1) `ZINC001459801531.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459801531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459801531/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001459801531 none CC(C)(NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(OC(F)(F)F)cc1 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', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', '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, 12, 5, 15, 15, 15, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 12, 5, 10, 42, 42, 42, 42, 12, 12, 5, 5, 5, 5, 5, 5, 3, 5, 5, 12, 12, 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459801531 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459801531 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459801531/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459801531/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459801531 Building ZINC001459833618 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459833618' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459833618 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459833618 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459833618/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459833618 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/34 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/34' -> `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(C)c(Br)c(C)c1) `ZINC001459833618.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459833618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459833618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001459833618 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(C)c(Br)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', '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'] 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, 5, 1, 17, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 16, 16, 5, 16, 16, 5, 5, 1, 1, 1, 1, 9, 9, 9, 25, 25, 25, 17, 25, 25, 25, 25, 5, 5, 5, 16, 16, 5, 16, 16, 5, 5, 5, 9, 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]) total number of confs: 122 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459833618 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459833618/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459833618 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 35) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/35 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/35' -> `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(C)c(Br)c(C)c1) `ZINC001459833618.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459833618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459833618/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001459833618 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(C)c(Br)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', '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'] 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, 5, 1, 17, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 17, 17, 6, 17, 17, 6, 6, 1, 1, 1, 1, 8, 8, 8, 25, 25, 25, 10, 16, 25, 25, 25, 6, 6, 6, 17, 17, 6, 17, 17, 6, 6, 6, 8, 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]) total number of confs: 125 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459833618 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459833618 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459833618/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459833618/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459833618 Building ZINC001459833618 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459833618' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459833618 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459833618 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459833618/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459833618 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 34) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(C)c(Br)c(C)c1) `ZINC001459833618.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459833618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459833618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001459833618 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(C)c(Br)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', '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'] 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, 5, 1, 17, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 16, 16, 5, 16, 16, 5, 5, 1, 1, 1, 1, 9, 9, 9, 25, 25, 25, 17, 25, 25, 25, 25, 5, 5, 5, 16, 16, 5, 16, 16, 5, 5, 5, 9, 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]) total number of confs: 122 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459833618 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459833618/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459833618 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 35) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(C)c(Br)c(C)c1) `ZINC001459833618.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459833618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459833618/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001459833618 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(C)c(Br)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', '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'] 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, 5, 1, 17, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 17, 17, 6, 17, 17, 6, 6, 1, 1, 1, 1, 8, 8, 8, 25, 25, 25, 10, 16, 25, 25, 25, 6, 6, 6, 17, 17, 6, 17, 17, 6, 6, 6, 8, 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]) total number of confs: 125 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459833618 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459833618 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459833618/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459833618/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459833618 Building ZINC001459978468 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459978468' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459978468 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459978468 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459978468/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459978468 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/36 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2nccnc2c1Br)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001459978468.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459978468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459978468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459978468 none O=C(Nc1ccc2nccnc2c1Br)[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', 'N.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 17, 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, 3, 7, 7, 3, 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: [9, 1, 9, 9, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 9, 35, 35, 35, 35, 6, 1, 6] 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459978468 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459978468/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459978468 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 37) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/37 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/37' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2nccnc2c1Br)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001459978468.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459978468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459978468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459978468 none O=C(Nc1ccc2nccnc2c1Br)[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', 'N.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 17, 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, 3, 7, 7, 3, 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: [9, 1, 9, 9, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 9, 35, 35, 35, 35, 6, 1, 6] 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459978468 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459978468 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459978468/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459978468/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459978468 Building ZINC001459978468 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459978468' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459978468 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459978468 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459978468/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459978468 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 36) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ccc2nccnc2c1Br)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001459978468.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459978468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459978468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459978468 none O=C(Nc1ccc2nccnc2c1Br)[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', 'N.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 17, 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, 3, 7, 7, 3, 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: [9, 1, 9, 9, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 9, 35, 35, 35, 35, 6, 1, 6] 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459978468 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459978468/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459978468 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 37) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ccc2nccnc2c1Br)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001459978468.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459978468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459978468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459978468 none O=C(Nc1ccc2nccnc2c1Br)[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', 'N.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 17, 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, 3, 7, 7, 3, 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: [9, 1, 9, 9, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 9, 35, 35, 35, 35, 6, 1, 6] 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459978468 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001459978468 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459978468/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459978468/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001459978468 Building ZINC001460008735 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460008735' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460008735 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460008735 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460008735/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460008735 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/38 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c2cc(Br)ccc21) `ZINC001460008735.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460008735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460008735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001460008735 none CC1(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c2cc(Br)ccc21 NO_LONG_NAME dock atom types: ['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', 'C.ar', 'Br', '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, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 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, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 3, 17, 1, 1, 1, 9, 9, 9, 9, 18, 18, 9, 18, 18, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 18, 18, 9, 18, 18, 9, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460008735 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460008735/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460008735 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 39) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/39 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/39' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c2cc(Br)ccc21) `ZINC001460008735.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460008735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460008735/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001460008735 none CC1(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c2cc(Br)ccc21 NO_LONG_NAME dock atom types: ['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', 'C.ar', 'Br', '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, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 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, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 3, 18, 1, 1, 1, 9, 9, 9, 9, 22, 22, 9, 22, 22, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 22, 22, 9, 22, 22, 9, 19, 19, 19] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460008735 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460008735 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460008735/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460008735/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460008735 Building ZINC001460008735 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460008735' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460008735 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460008735 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460008735/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460008735 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 38) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC1(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c2cc(Br)ccc21) `ZINC001460008735.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460008735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460008735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001460008735 none CC1(C)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c2cc(Br)ccc21 NO_LONG_NAME dock atom types: ['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', 'C.ar', 'Br', '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, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 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, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 3, 17, 1, 1, 1, 9, 9, 9, 9, 18, 18, 9, 18, 18, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 18, 18, 9, 18, 18, 9, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460008735 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460008735/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460008735 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 39) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC1(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c2cc(Br)ccc21) `ZINC001460008735.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460008735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460008735/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001460008735 none CC1(C)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c2cc(Br)ccc21 NO_LONG_NAME dock atom types: ['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', 'C.ar', 'Br', '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, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 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, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 3, 18, 1, 1, 1, 9, 9, 9, 9, 22, 22, 9, 22, 22, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 22, 22, 9, 22, 22, 9, 19, 19, 19] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460008735 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460008735 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460008735/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460008735/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460008735 Building ZINC001460010453 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010453' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010453 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460010453 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010453/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010453 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/40 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(Cl)c(Cl)c1) `ZINC001460010453.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460010453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460010453 none COCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', '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'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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] 0 hydrogens 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, 7, 4, 3, 4, 3, 1, 3, 1, 1, 1, 5, 5, 2, 5, 9, 5, 5, 5, 4, 12, 12, 7, 12, 12, 12, 12, 13, 13, 13, 9, 9, 7, 7, 3, 5, 5, 9, 9, 9, 5, 12, 12, 12] 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: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010453 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010453/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010453 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 41) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/41 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/41' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(Cl)c(Cl)c1) `ZINC001460010453.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460010453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010453/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460010453 none COCC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', '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'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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] 0 hydrogens 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, 12, 10, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 9, 4, 4, 4, 4, 12, 12, 8, 12, 12, 12, 12, 16, 16, 16, 12, 12, 10, 10, 2, 4, 4, 9, 9, 9, 4, 12, 12, 12] 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: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010453 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460010453 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010453/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010453/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010453 Building ZINC001460010453 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010453' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010453 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460010453 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010453/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010453 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 40) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(Cl)c(Cl)c1) `ZINC001460010453.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460010453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460010453 none COCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', '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'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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] 0 hydrogens 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, 7, 4, 3, 4, 3, 1, 3, 1, 1, 1, 5, 5, 2, 5, 9, 5, 5, 5, 4, 12, 12, 7, 12, 12, 12, 12, 13, 13, 13, 9, 9, 7, 7, 3, 5, 5, 9, 9, 9, 5, 12, 12, 12] 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: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010453 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010453/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010453 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 41) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COCC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(Cl)c(Cl)c1) `ZINC001460010453.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460010453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010453/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460010453 none COCC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', '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'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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] 0 hydrogens 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, 12, 10, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 9, 4, 4, 4, 4, 12, 12, 8, 12, 12, 12, 12, 16, 16, 16, 12, 12, 10, 10, 2, 4, 4, 9, 9, 9, 4, 12, 12, 12] 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: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010453 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460010453 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010453/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010453/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010453 Building ZINC001460010455 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010455' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010455 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460010455 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010455/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010455 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/42 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(Cl)c(Cl)c1) `ZINC001460010455.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460010455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460010455 none COCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', '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'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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] 0 hydrogens 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, 12, 10, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 9, 4, 4, 4, 4, 12, 12, 8, 12, 12, 12, 12, 16, 16, 16, 12, 12, 10, 10, 2, 4, 4, 9, 9, 9, 4, 12, 12, 12] 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: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010455 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010455/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010455 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 43) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/43 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/43' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(Cl)c(Cl)c1) `ZINC001460010455.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460010455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460010455 none COCC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', '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'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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] 0 hydrogens 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, 7, 4, 3, 4, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 10, 6, 6, 6, 4, 13, 13, 8, 13, 13, 13, 13, 13, 13, 13, 9, 9, 7, 7, 3, 6, 6, 10, 10, 10, 6, 13, 13, 13] 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: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010455 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460010455 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010455/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010455/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010455 Building ZINC001460010455 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010455' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010455 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460010455 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010455/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010455 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 42) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(Cl)c(Cl)c1) `ZINC001460010455.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460010455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460010455 none COCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', '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'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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] 0 hydrogens 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, 12, 10, 4, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 9, 4, 4, 4, 4, 12, 12, 8, 12, 12, 12, 12, 16, 16, 16, 12, 12, 10, 10, 2, 4, 4, 9, 9, 9, 4, 12, 12, 12] 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: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010455 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010455/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010455 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 43) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COCC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(Cl)c(Cl)c1) `ZINC001460010455.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460010455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460010455 none COCC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', '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'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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] 0 hydrogens 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, 7, 4, 3, 4, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 10, 6, 6, 6, 4, 13, 13, 8, 13, 13, 13, 13, 13, 13, 13, 9, 9, 7, 7, 3, 6, 6, 10, 10, 10, 6, 13, 13, 13] 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: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010455 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460010455 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010455/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010455/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460010455 Building ZINC001460033078 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460033078' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460033078 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460033078 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460033078/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460033078 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/44 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)cc(Oc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2)c1) `ZINC001460033078.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460033078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460033078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460033078 none COc1cc(OC)cc(Oc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', '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', 'Cl', 'S.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'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 50, 50, 50, 50, 48, 20, 12, 33, 33, 12, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 33, 33, 50, 50, 50, 50, 48, 50, 50, 50, 50, 33, 33, 12, 12, 2, 2, 2, 33, 33, 50] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460033078 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460033078/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460033078 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 45) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/45 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/45' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)cc(Oc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2)c1) `ZINC001460033078.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460033078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460033078/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460033078 none COc1cc(OC)cc(Oc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', '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', 'Cl', 'S.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'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 33, 15, 33, 33, 12, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 12, 12, 2, 2, 2, 33, 33, 50] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460033078 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460033078 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460033078/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460033078/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460033078 Building ZINC001460033078 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460033078' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460033078 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460033078 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460033078/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460033078 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 44) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1cc(OC)cc(Oc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2)c1) `ZINC001460033078.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460033078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460033078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460033078 none COc1cc(OC)cc(Oc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', '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', 'Cl', 'S.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'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 50, 50, 50, 50, 48, 20, 12, 33, 33, 12, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 33, 33, 50, 50, 50, 50, 48, 50, 50, 50, 50, 33, 33, 12, 12, 2, 2, 2, 33, 33, 50] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460033078 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460033078/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460033078 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 45) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1cc(OC)cc(Oc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2)c1) `ZINC001460033078.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460033078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460033078/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460033078 none COc1cc(OC)cc(Oc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', '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', 'Cl', 'S.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'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 33, 15, 33, 33, 12, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 12, 12, 2, 2, 2, 33, 33, 50] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460033078 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460033078 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460033078/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460033078/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460033078 Building ZINC001460091594 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460091594' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460091594 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460091594 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460091594/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460091594 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/46 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2(c3ccccc3Br)CCCCC2)cn1) `ZINC001460091594.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460091594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460091594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460091594 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2(c3ccccc3Br)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 17, 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] 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] 0 hydrogens 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, 14, 14, 10, 10, 1, 1, 1, 1, 4, 4, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 10, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460091594 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460091594/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460091594 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 47) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/47 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/47' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2(c3ccccc3Br)CCCCC2)cn1) `ZINC001460091594.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460091594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460091594/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460091594 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2(c3ccccc3Br)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 17, 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] 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] 0 hydrogens 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, 14, 14, 10, 10, 1, 1, 1, 1, 4, 4, 7, 15, 17, 17, 17, 17, 17, 17, 15, 15, 15, 15, 15, 10, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 10, 4, 17, 17, 17, 17, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/12845/xbi-8058088.35/working/building/ZINC001460091594 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460091594 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460091594/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460091594/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460091594 Building ZINC001460091594 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460091594' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460091594 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460091594 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460091594/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460091594 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 46) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2(c3ccccc3Br)CCCCC2)cn1) `ZINC001460091594.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460091594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460091594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460091594 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NC2(c3ccccc3Br)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 17, 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] 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] 0 hydrogens 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, 14, 14, 10, 10, 1, 1, 1, 1, 4, 4, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 10, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460091594 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460091594/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460091594 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 47) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2(c3ccccc3Br)CCCCC2)cn1) `ZINC001460091594.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460091594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460091594/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460091594 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NC2(c3ccccc3Br)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 17, 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] 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] 0 hydrogens 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, 14, 14, 10, 10, 1, 1, 1, 1, 4, 4, 7, 15, 17, 17, 17, 17, 17, 17, 15, 15, 15, 15, 15, 10, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 10, 4, 17, 17, 17, 17, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/12845/xbi-8058088.35/working/building/ZINC001460091594 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460091594 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460091594/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460091594/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460091594 Building ZINC001460183362 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460183362' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460183362 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460183362 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460183362/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460183362 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/48 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(c1ccc(Br)cc1)C1CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001460183362.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460183362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460183362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001460183362 none O=C(N(c1ccc(Br)cc1)C1CC1)[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', 'Br', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [6, 1, 6, 13, 26, 26, 18, 26, 26, 26, 13, 26, 26, 1, 1, 1, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9, 9] 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]) total number of confs: 145 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460183362 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460183362/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460183362 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 49) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/49 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/49' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(c1ccc(Br)cc1)C1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001460183362.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460183362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460183362/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001460183362 none O=C(N(c1ccc(Br)cc1)C1CC1)[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', 'Br', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [6, 1, 6, 12, 27, 27, 19, 27, 27, 27, 12, 26, 26, 1, 1, 1, 8, 8, 8, 8, 8, 27, 27, 27, 27, 26, 26, 26, 26, 26, 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]) total number of confs: 138 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460183362 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460183362 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460183362/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460183362/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460183362 Building ZINC001460183362 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460183362' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460183362 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460183362 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460183362/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460183362 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 48) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N(c1ccc(Br)cc1)C1CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001460183362.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460183362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460183362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001460183362 none O=C(N(c1ccc(Br)cc1)C1CC1)[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', 'Br', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [6, 1, 6, 13, 26, 26, 18, 26, 26, 26, 13, 26, 26, 1, 1, 1, 9, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9, 9] 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]) total number of confs: 145 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460183362 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460183362/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460183362 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 49) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N(c1ccc(Br)cc1)C1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001460183362.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460183362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460183362/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001460183362 none O=C(N(c1ccc(Br)cc1)C1CC1)[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', 'Br', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [6, 1, 6, 12, 27, 27, 19, 27, 27, 27, 12, 26, 26, 1, 1, 1, 8, 8, 8, 8, 8, 27, 27, 27, 27, 26, 26, 26, 26, 26, 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]) total number of confs: 138 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460183362 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460183362 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460183362/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460183362/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460183362 Building ZINC001460220470 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460220470' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460220470 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460220470 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460220470/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460220470 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/50 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(F)(Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001460220470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460220470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460220470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001460220470 none O=C(N1CCC(F)(Cc2ccc(Cl)cc2)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', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 15, 5, 1, 1, 1, 1, 16, 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, 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: [7, 2, 10, 16, 16, 16, 16, 16, 33, 33, 33, 33, 33, 33, 33, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 16, 16, 16, 16, 33, 33, 33, 33, 33, 33, 16, 16, 16, 16, 4, 4] 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: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460220470 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460220470/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460220470 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 51) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/51 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/51' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(F)(Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001460220470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460220470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460220470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001460220470 none O=C(N1CCC(F)(Cc2ccc(Cl)cc2)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', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 15, 5, 1, 1, 1, 1, 16, 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, 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: [7, 2, 10, 15, 15, 15, 15, 15, 34, 34, 34, 34, 34, 34, 34, 15, 15, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 15, 34, 34, 34, 34, 34, 34, 15, 15, 15, 15, 4, 4] 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: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460220470 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460220470 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460220470/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460220470/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460220470 Building ZINC001460220470 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460220470' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460220470 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460220470 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460220470/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460220470 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 50) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CCC(F)(Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001460220470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460220470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460220470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001460220470 none O=C(N1CCC(F)(Cc2ccc(Cl)cc2)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', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 15, 5, 1, 1, 1, 1, 16, 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, 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: [7, 2, 10, 16, 16, 16, 16, 16, 33, 33, 33, 33, 33, 33, 33, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 16, 16, 16, 16, 33, 33, 33, 33, 33, 33, 16, 16, 16, 16, 4, 4] 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: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460220470 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460220470/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460220470 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 51) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CCC(F)(Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001460220470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460220470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460220470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001460220470 none O=C(N1CCC(F)(Cc2ccc(Cl)cc2)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', 'F', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 15, 5, 1, 1, 1, 1, 16, 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, 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: [7, 2, 10, 15, 15, 15, 15, 15, 34, 34, 34, 34, 34, 34, 34, 15, 15, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 15, 15, 34, 34, 34, 34, 34, 34, 15, 15, 15, 15, 4, 4] 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: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460220470 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460220470 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460220470/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460220470/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460220470 Building ZINC001460348143 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460348143' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460348143 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460348143 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460348143/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460348143 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/52 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc(Br)cc2Cl)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001460348143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460348143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460348143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460348143 none O=C(NCC1(c2ccc(Br)cc2Cl)CC1)[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', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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, 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: [2, 1, 2, 2, 14, 34, 35, 35, 35, 35, 35, 35, 35, 34, 34, 1, 1, 1, 7, 7, 7, 7, 7, 2, 14, 14, 35, 35, 35, 34, 34, 34, 34, 7, 7] 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460348143 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460348143/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460348143 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 53) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/53 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/53' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc(Br)cc2Cl)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001460348143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460348143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460348143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460348143 none O=C(NCC1(c2ccc(Br)cc2Cl)CC1)[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', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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, 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: [2, 1, 2, 2, 14, 33, 34, 34, 34, 34, 34, 34, 34, 33, 33, 1, 1, 1, 7, 7, 7, 7, 7, 2, 14, 14, 34, 34, 34, 33, 33, 33, 33, 7, 7] 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460348143 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460348143 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460348143/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460348143/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460348143 Building ZINC001460348143 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460348143' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460348143 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460348143 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460348143/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460348143 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 52) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(NCC1(c2ccc(Br)cc2Cl)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001460348143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460348143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460348143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460348143 none O=C(NCC1(c2ccc(Br)cc2Cl)CC1)[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', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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, 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: [2, 1, 2, 2, 14, 34, 35, 35, 35, 35, 35, 35, 35, 34, 34, 1, 1, 1, 7, 7, 7, 7, 7, 2, 14, 14, 35, 35, 35, 34, 34, 34, 34, 7, 7] 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460348143 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460348143/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460348143 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 53) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(NCC1(c2ccc(Br)cc2Cl)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001460348143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460348143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460348143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460348143 none O=C(NCC1(c2ccc(Br)cc2Cl)CC1)[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', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 17, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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, 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: [2, 1, 2, 2, 14, 33, 34, 34, 34, 34, 34, 34, 34, 33, 33, 1, 1, 1, 7, 7, 7, 7, 7, 2, 14, 14, 34, 34, 34, 33, 33, 33, 33, 7, 7] 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460348143 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460348143 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460348143/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460348143/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460348143 Building ZINC001460352210 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460352210' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460352210 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460352210 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460352210/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460352210 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/54 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc(Br)cc2Cl)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001460352210.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460352210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460352210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460352210 none O=C(NCC1(c2ccc(Br)cc2Cl)CC1)[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', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 16, 5, 5, 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] 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, 7, 7, 7, 7] 0 hydrogens need rotated 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, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 14, 14, 28, 28, 28, 28, 28, 28, 28, 6, 6, 6, 6, 6, 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: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460352210 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460352210/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460352210 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 55) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/55 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/55' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2ccc(Br)cc2Cl)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001460352210.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460352210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460352210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460352210 none O=C(NCC1(c2ccc(Br)cc2Cl)CC1)[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', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 16, 5, 5, 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] 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, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 26, 27, 27, 26, 27, 27, 27, 27, 26, 26, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 12, 12, 27, 27, 27, 26, 26, 26, 26, 6, 6, 6, 6, 6, 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: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460352210 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460352210 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460352210/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460352210/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460352210 Building ZINC001460352210 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460352210' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460352210 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460352210 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460352210/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460352210 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 54) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(NCC1(c2ccc(Br)cc2Cl)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001460352210.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460352210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460352210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460352210 none O=C(NCC1(c2ccc(Br)cc2Cl)CC1)[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', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 16, 5, 5, 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] 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, 7, 7, 7, 7] 0 hydrogens need rotated 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, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 14, 14, 28, 28, 28, 28, 28, 28, 28, 6, 6, 6, 6, 6, 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: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460352210 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460352210/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460352210 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 55) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(NCC1(c2ccc(Br)cc2Cl)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001460352210.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460352210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460352210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460352210 none O=C(NCC1(c2ccc(Br)cc2Cl)CC1)[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', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 16, 5, 5, 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] 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, 7, 7, 7, 7] 0 hydrogens need rotated 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, 12, 26, 27, 27, 26, 27, 27, 27, 27, 26, 26, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 2, 12, 12, 27, 27, 27, 26, 26, 26, 26, 6, 6, 6, 6, 6, 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: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460352210 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460352210 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460352210/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460352210/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460352210 Building ZINC001460384947 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460384947' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460384947 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460384947 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460384947/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460384947 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/56 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(S(=O)(=O)C2CCCCC2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001460384947.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460384947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460384947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460384947 none O=C(Nc1cccc(S(=O)(=O)C2CCCCC2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 14, 14, 14, 14, 21, 21, 25, 49, 49, 49, 49, 49, 14, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 14, 14, 14, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 14, 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, 41, 42, 43, 44, 45, 46]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460384947 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460384947/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460384947 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 57) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/57 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/57' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(S(=O)(=O)C2CCCCC2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001460384947.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460384947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460384947/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460384947 none O=C(Nc1cccc(S(=O)(=O)C2CCCCC2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 2, 13, 13, 20, 20, 24, 48, 48, 48, 48, 48, 13, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 13, 13, 4, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 13, 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, 41, 42, 43, 44, 45, 46]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460384947 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460384947 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460384947/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460384947/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460384947 Building ZINC001460384947 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460384947' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460384947 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460384947 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460384947/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460384947 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 56) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/56: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(S(=O)(=O)C2CCCCC2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001460384947.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460384947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460384947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460384947 none O=C(Nc1cccc(S(=O)(=O)C2CCCCC2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 14, 14, 14, 14, 21, 21, 25, 49, 49, 49, 49, 49, 14, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 14, 14, 14, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 14, 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, 41, 42, 43, 44, 45, 46]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460384947 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460384947/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460384947 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 57) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/57: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(S(=O)(=O)C2CCCCC2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001460384947.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460384947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460384947/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460384947 none O=C(Nc1cccc(S(=O)(=O)C2CCCCC2)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', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 5, 5, 5, 1, 5, 12, 1, 1, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 2, 13, 13, 20, 20, 24, 48, 48, 48, 48, 48, 13, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 13, 13, 4, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 13, 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, 41, 42, 43, 44, 45, 46]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460384947 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460384947 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460384947/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460384947/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460384947 Building ZINC001460388820 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460388820' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460388820 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460388820 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460388820/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460388820 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/58 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001460388820.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460388820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460388820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001460388820 none O=C(N(Cc1ccncc1)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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', 'Cl', '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, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 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, 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: [6, 1, 6, 13, 35, 48, 48, 43, 48, 48, 13, 28, 28, 21, 28, 28, 28, 1, 1, 1, 4, 4, 1, 1, 4, 4, 35, 35, 48, 48, 48, 48, 28, 28, 28, 28, 4, 4, 4, 4] 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]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460388820 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460388820/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460388820 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 59) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/59 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/59' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001460388820.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460388820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460388820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001460388820 none O=C(N(Cc1ccncc1)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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', 'Cl', '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, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 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, 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: [6, 1, 6, 12, 35, 48, 48, 48, 48, 48, 12, 26, 26, 18, 26, 26, 26, 1, 1, 1, 4, 4, 1, 1, 4, 4, 35, 35, 48, 48, 48, 48, 26, 26, 26, 26, 4, 4, 4, 4] 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]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460388820 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460388820 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460388820/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460388820/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460388820 Building ZINC001460388820 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460388820' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460388820 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460388820 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460388820/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460388820 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 58) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/58: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001460388820.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460388820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460388820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001460388820 none O=C(N(Cc1ccncc1)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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', 'Cl', '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, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 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, 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: [6, 1, 6, 13, 35, 48, 48, 43, 48, 48, 13, 28, 28, 21, 28, 28, 28, 1, 1, 1, 4, 4, 1, 1, 4, 4, 35, 35, 48, 48, 48, 48, 28, 28, 28, 28, 4, 4, 4, 4] 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]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460388820 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460388820/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460388820 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 59) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/59: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccncc1)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001460388820.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460388820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460388820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001460388820 none O=C(N(Cc1ccncc1)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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', 'Cl', '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, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 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, 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: [6, 1, 6, 12, 35, 48, 48, 48, 48, 48, 12, 26, 26, 18, 26, 26, 26, 1, 1, 1, 4, 4, 1, 1, 4, 4, 35, 35, 48, 48, 48, 48, 26, 26, 26, 26, 4, 4, 4, 4] 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]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460388820 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460388820 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460388820/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460388820/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460388820 Building ZINC001460462215 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462215' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462215 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460462215 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462215/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462215 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/60 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@@H]1Cc1ccccc1Br)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001460462215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460462215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001460462215 none O=C(N1CCCC[C@@H]1Cc1ccccc1Br)[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', 'C.3', 'H', 'C.3', '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', '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, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 1, 16, 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: [8, 1, 8, 11, 11, 11, 11, 11, 11, 11, 22, 29, 29, 24, 29, 29, 29, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 22, 22, 29, 29, 29, 29, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 121 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462215 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462215/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462215 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 61) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/61 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/61' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@@H]1Cc1ccccc1Br)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001460462215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460462215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001460462215 none O=C(N1CCCC[C@@H]1Cc1ccccc1Br)[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', 'C.3', 'H', 'C.3', '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', '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, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 1, 16, 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: [7, 1, 7, 12, 12, 12, 12, 12, 12, 12, 21, 28, 28, 21, 28, 28, 28, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 21, 21, 28, 28, 28, 28, 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]) total number of confs: 127 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462215 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460462215 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462215/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462215/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462215 Building ZINC001460462215 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462215' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462215 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460462215 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462215/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462215 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 60) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(N1CCCC[C@@H]1Cc1ccccc1Br)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001460462215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460462215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001460462215 none O=C(N1CCCC[C@@H]1Cc1ccccc1Br)[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', 'C.3', 'H', 'C.3', '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', '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, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 1, 16, 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: [8, 1, 8, 11, 11, 11, 11, 11, 11, 11, 22, 29, 29, 24, 29, 29, 29, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 22, 22, 29, 29, 29, 29, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 121 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462215 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462215/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462215 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 61) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(N1CCCC[C@@H]1Cc1ccccc1Br)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001460462215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460462215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001460462215 none O=C(N1CCCC[C@@H]1Cc1ccccc1Br)[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', 'C.3', 'H', 'C.3', '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', '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, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 1, 16, 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: [7, 1, 7, 12, 12, 12, 12, 12, 12, 12, 21, 28, 28, 21, 28, 28, 28, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 21, 21, 28, 28, 28, 28, 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]) total number of confs: 127 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462215 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460462215 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462215/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462215/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462215 Building ZINC001460462218 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462218' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460462218 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462218/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/62 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@H]1Cc1ccccc1Br)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001460462218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460462218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001460462218 none O=C(N1CCCC[C@H]1Cc1ccccc1Br)[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', 'C.3', 'H', 'C.3', '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', '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, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 1, 16, 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: [7, 1, 7, 12, 12, 12, 12, 12, 12, 12, 21, 27, 27, 21, 27, 27, 27, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 21, 21, 27, 27, 27, 27, 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]) total number of confs: 120 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462218/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 63) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/63 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/63' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC[C@H]1Cc1ccccc1Br)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001460462218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460462218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001460462218 none O=C(N1CCCC[C@H]1Cc1ccccc1Br)[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', 'C.3', 'H', 'C.3', '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', '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, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 1, 16, 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: [8, 1, 8, 11, 11, 11, 11, 11, 11, 11, 21, 27, 27, 21, 27, 27, 27, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 27, 27, 26, 27, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 119 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460462218 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462218/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462218/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462218 Building ZINC001460462218 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462218' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460462218 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462218/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 62) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(N1CCCC[C@H]1Cc1ccccc1Br)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001460462218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460462218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001460462218 none O=C(N1CCCC[C@H]1Cc1ccccc1Br)[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', 'C.3', 'H', 'C.3', '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', '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, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 1, 16, 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: [7, 1, 7, 12, 12, 12, 12, 12, 12, 12, 21, 27, 27, 21, 27, 27, 27, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 21, 21, 27, 27, 27, 27, 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]) total number of confs: 120 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462218/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 63) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(N1CCCC[C@H]1Cc1ccccc1Br)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001460462218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460462218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001460462218 none O=C(N1CCCC[C@H]1Cc1ccccc1Br)[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', 'C.3', 'H', 'C.3', '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', '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, 5, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 1, 16, 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: [8, 1, 8, 11, 11, 11, 11, 11, 11, 11, 21, 27, 27, 21, 27, 27, 27, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 27, 27, 26, 27, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 119 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460462218 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462218/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462218/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460462218 Building ZINC001460584279 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460584279' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460584279 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460584279 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460584279/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460584279 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/64 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Cc1cccc(F)c1)c1cc(Cl)cnc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001460584279.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460584279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460584279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460584279 none O=C(Cc1cccc(F)c1)c1cc(Cl)cnc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 10, 32, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 32, 32, 50, 50, 50, 50, 7, 7, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 147 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460584279 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460584279/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460584279 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 65) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/65 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/65' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Cc1cccc(F)c1)c1cc(Cl)cnc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001460584279.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460584279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460584279/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460584279 none O=C(Cc1cccc(F)c1)c1cc(Cl)cnc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 10, 32, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 32, 32, 50, 50, 50, 50, 7, 7, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460584279 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460584279 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460584279/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460584279/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460584279 Building ZINC001460584279 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460584279' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460584279 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460584279 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460584279/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460584279 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 64) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Cc1cccc(F)c1)c1cc(Cl)cnc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001460584279.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460584279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460584279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460584279 none O=C(Cc1cccc(F)c1)c1cc(Cl)cnc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 10, 32, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 32, 32, 50, 50, 50, 50, 7, 7, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 147 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460584279 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460584279/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460584279 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 65) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Cc1cccc(F)c1)c1cc(Cl)cnc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001460584279.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460584279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460584279/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460584279 none O=C(Cc1cccc(F)c1)c1cc(Cl)cnc1NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 10, 32, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 32, 32, 50, 50, 50, 50, 7, 7, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460584279 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460584279 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460584279/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460584279/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460584279 Building ZINC001460657451 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657451' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657451 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460657451 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657451/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657451 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/66 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCCCC1)OC[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001460657451.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460657451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001460657451 none O=C(NC1CCCCC1)OC[C@H]1CCCCN1C(=O)[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', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 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, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 50, 50, 50, 50, 50, 8, 3, 3, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 2, 1, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657451 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657451/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657451 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 67) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/67 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/67' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCCCC1)OC[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001460657451.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460657451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657451/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001460657451 none O=C(NC1CCCCC1)OC[C@H]1CCCCN1C(=O)[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', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 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, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 50, 50, 50, 50, 50, 8, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 2, 1, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 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/12845/xbi-8058088.35/working/building/ZINC001460657451 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460657451 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657451/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657451/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657451 Building ZINC001460657451 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657451' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657451 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460657451 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657451/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657451 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 66) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NC1CCCCC1)OC[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001460657451.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460657451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001460657451 none O=C(NC1CCCCC1)OC[C@H]1CCCCN1C(=O)[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', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 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, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 50, 50, 50, 50, 50, 8, 3, 3, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 2, 1, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657451 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657451/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657451 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 67) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NC1CCCCC1)OC[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001460657451.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460657451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657451/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001460657451 none O=C(NC1CCCCC1)OC[C@H]1CCCCN1C(=O)[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', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 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, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 50, 50, 50, 50, 50, 8, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 2, 1, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 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/12845/xbi-8058088.35/working/building/ZINC001460657451 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460657451 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657451/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657451/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657451 Building ZINC001460657454 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657454' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657454 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460657454 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657454/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657454 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/68 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCCCC1)OC[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001460657454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460657454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001460657454 none O=C(NC1CCCCC1)OC[C@@H]1CCCCN1C(=O)[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', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 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, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 50, 50, 50, 50, 50, 8, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 2, 1, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 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/12845/xbi-8058088.35/working/building/ZINC001460657454 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657454/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657454 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 69) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/69 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/69' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCCCC1)OC[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001460657454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460657454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001460657454 none O=C(NC1CCCCC1)OC[C@@H]1CCCCN1C(=O)[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', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 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, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 29, 50, 50, 50, 50, 50, 8, 3, 3, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 2, 1, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657454 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460657454 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657454/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657454/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657454 Building ZINC001460657454 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657454' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657454 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460657454 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657454/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657454 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 68) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NC1CCCCC1)OC[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001460657454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460657454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001460657454 none O=C(NC1CCCCC1)OC[C@@H]1CCCCN1C(=O)[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', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 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, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 50, 50, 50, 50, 50, 8, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 2, 1, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 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/12845/xbi-8058088.35/working/building/ZINC001460657454 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657454/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657454 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 69) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NC1CCCCC1)OC[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001460657454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460657454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001460657454 none O=C(NC1CCCCC1)OC[C@@H]1CCCCN1C(=O)[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', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 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, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 29, 50, 50, 50, 50, 50, 8, 3, 3, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 2, 1, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657454 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460657454 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657454/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657454/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460657454 Building ZINC001460705106 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460705106' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460705106 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460705106 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460705106/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460705106 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/70 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(C2CCC2)CCC1) `ZINC001460705106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460705106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460705106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001460705106 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(C2CCC2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 11, 17, 17, 17, 11, 11, 11, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 6, 6, 17, 17, 17, 17, 17, 17, 17, 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: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460705106 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460705106/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460705106 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 71) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/71 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/71' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(C2CCC2)CCC1) `ZINC001460705106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460705106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460705106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001460705106 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(C2CCC2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 10, 16, 16, 16, 10, 10, 10, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 16, 16, 16, 16, 16, 16, 16, 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, 56]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460705106 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460705106 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460705106/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460705106/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460705106 Building ZINC001460705106 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460705106' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460705106 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460705106 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460705106/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460705106 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 70) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/70: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(C2CCC2)CCC1) `ZINC001460705106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460705106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460705106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001460705106 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(C2CCC2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 11, 17, 17, 17, 11, 11, 11, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 6, 6, 17, 17, 17, 17, 17, 17, 17, 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: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460705106 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460705106/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460705106 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 71) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/71: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(C2CCC2)CCC1) `ZINC001460705106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460705106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460705106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001460705106 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(C2CCC2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 10, 16, 16, 16, 10, 10, 10, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 16, 16, 16, 16, 16, 16, 16, 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, 56]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460705106 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460705106 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460705106/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460705106/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460705106 Building ZINC001460707459 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460707459' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460707459 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460707459 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460707459/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460707459 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/72 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/72' -> `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)(C)C1=CCCC1) `ZINC001460707459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460707459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460707459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001460707459 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)C1=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.3', 'F', '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.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 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, 1, 1, 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, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 15, 14, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460707459 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460707459/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460707459 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 73) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/73 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/73' -> `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)(C)C1=CCCC1) `ZINC001460707459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460707459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460707459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001460707459 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(C)(C)C1=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.3', 'F', '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.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 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, 1, 1, 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, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 14, 13, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460707459 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460707459 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460707459/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460707459/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460707459 Building ZINC001460707459 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460707459' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460707459 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460707459 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460707459/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460707459 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 72) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/72: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)C1=CCCC1) `ZINC001460707459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460707459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460707459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001460707459 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)C1=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.3', 'F', '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.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 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, 1, 1, 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, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 15, 14, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460707459 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460707459/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460707459 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 73) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/73: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(C)(C)C1=CCCC1) `ZINC001460707459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460707459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460707459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001460707459 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(C)(C)C1=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.3', 'F', '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.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 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, 1, 1, 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, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 14, 13, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460707459 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460707459 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460707459/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460707459/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460707459 Building ZINC001460729819 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729819' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729819 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460729819 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729819/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729819 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/74 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2c2nc3ccc(Cl)cc3[nH]2)cc1Cl) `ZINC001460729819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460729819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001460729819 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2c2nc3ccc(Cl)cc3[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', '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, 5, 5, 7, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 6, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 2, 5, 5, 1, 1, 1, 2, 7, 7, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 5, 5, 10, 10, 10, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27, 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729819 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729819/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729819 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 75) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/75 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/75' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2c2nc3ccc(Cl)cc3[nH]2)cc1Cl) `ZINC001460729819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460729819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001460729819 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2c2nc3ccc(Cl)cc3[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', '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, 5, 5, 7, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 6, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 2, 6, 6, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 10, 10, 10, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 25, 25, 25, 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729819 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460729819 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729819/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729819/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729819 Building ZINC001460729819 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729819' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729819 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460729819 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729819/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729819 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 74) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2c2nc3ccc(Cl)cc3[nH]2)cc1Cl) `ZINC001460729819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460729819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001460729819 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2c2nc3ccc(Cl)cc3[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', '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, 5, 5, 7, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 6, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 2, 5, 5, 1, 1, 1, 2, 7, 7, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 5, 5, 10, 10, 10, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27, 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729819 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729819/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729819 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 75) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2c2nc3ccc(Cl)cc3[nH]2)cc1Cl) `ZINC001460729819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460729819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001460729819 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2c2nc3ccc(Cl)cc3[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', '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, 5, 5, 7, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 6, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 2, 6, 6, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 10, 10, 10, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 25, 25, 25, 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729819 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460729819 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729819/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729819/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729819 Building ZINC001460729821 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729821' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729821 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460729821 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729821/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729821 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/76 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2c2nc3ccc(Cl)cc3[nH]2)cc1Cl) `ZINC001460729821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460729821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001460729821 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2c2nc3ccc(Cl)cc3[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', '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, 5, 5, 7, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 6, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 2, 5, 5, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 5, 5, 9, 9, 9, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 27, 27, 27, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 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/12845/xbi-8058088.35/working/building/ZINC001460729821 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729821/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729821 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 77) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/77 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/77' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2c2nc3ccc(Cl)cc3[nH]2)cc1Cl) `ZINC001460729821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460729821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001460729821 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2c2nc3ccc(Cl)cc3[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', '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, 5, 5, 7, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 6, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 2, 6, 6, 1, 1, 1, 2, 9, 9, 10, 10, 10, 10, 10, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 11, 11, 11, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 24, 24, 24, 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729821 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460729821 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729821/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729821/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729821 Building ZINC001460729821 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729821' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729821 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460729821 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729821/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729821 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 76) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2c2nc3ccc(Cl)cc3[nH]2)cc1Cl) `ZINC001460729821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460729821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001460729821 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2c2nc3ccc(Cl)cc3[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', '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, 5, 5, 7, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 6, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 2, 5, 5, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 5, 5, 9, 9, 9, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 27, 27, 27, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 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/12845/xbi-8058088.35/working/building/ZINC001460729821 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729821/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729821 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 77) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2c2nc3ccc(Cl)cc3[nH]2)cc1Cl) `ZINC001460729821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460729821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001460729821 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2c2nc3ccc(Cl)cc3[nH]2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', '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, 5, 5, 7, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 6, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 2, 6, 6, 1, 1, 1, 2, 9, 9, 10, 10, 10, 10, 10, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 11, 11, 11, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 24, 24, 24, 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729821 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460729821 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729821/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729821/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460729821 Building ZINC001460769569 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460769569' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460769569 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460769569 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460769569/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460769569 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/78 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=COc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC001460769569.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460769569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460769569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460769569 none C=COc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [1, 1, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 6, 6, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 8, 8, 22, 22, 22, 8, 8, 2, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 8, 8] 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: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460769569 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460769569/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460769569 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 79) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/79 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/79' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC001460769569.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460769569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460769569/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460769569 none C=COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [1, 1, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 8, 7, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 6, 16, 16, 16, 16, 16, 16, 3, 3, 8, 8, 18, 18, 18, 8, 8, 2, 3, 3, 3, 16, 16, 8, 16, 3, 3, 3, 8, 8] 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: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460769569 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460769569 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460769569/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460769569/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460769569 Building ZINC001460769569 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460769569' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460769569 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460769569 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460769569/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460769569 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 78) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C=COc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC001460769569.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460769569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460769569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460769569 none C=COc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [1, 1, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 6, 6, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 8, 8, 22, 22, 22, 8, 8, 2, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 8, 8] 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: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460769569 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460769569/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460769569 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 79) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C=COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC001460769569.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460769569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460769569/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001460769569 none C=COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [1, 1, 12, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 8, 7, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 6, 16, 16, 16, 16, 16, 16, 3, 3, 8, 8, 18, 18, 18, 8, 8, 2, 3, 3, 3, 16, 16, 8, 16, 3, 3, 3, 8, 8] 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: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460769569 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460769569 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460769569/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460769569/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460769569 Building ZINC001460868382 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460868382' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460868382 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460868382 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460868382/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460868382 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/80 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3c(Br)c(F)cc(F)c32)cc1Cl) `ZINC001460868382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460868382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460868382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001460868382 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3c(Br)c(F)cc(F)c32)cc1Cl NO_LONG_NAME dock atom 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', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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, 5, 5, 5, 1, 1, 17, 1, 15, 1, 1, 15, 1, 1, 1, 16, 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] 0 hydrogens 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, 2, 10, 10, 1, 1, 1, 3, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 10, 18, 18, 18, 10, 10, 17, 17, 17, 17, 17, 17, 17, 10] 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460868382 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460868382/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460868382 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 81) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/81 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/81' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3c(Br)c(F)cc(F)c32)cc1Cl) `ZINC001460868382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460868382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460868382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001460868382 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3c(Br)c(F)cc(F)c32)cc1Cl NO_LONG_NAME dock atom 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', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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, 5, 5, 5, 1, 1, 17, 1, 15, 1, 1, 15, 1, 1, 1, 16, 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] 0 hydrogens 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, 2, 10, 10, 1, 1, 1, 3, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 10, 10, 10, 18, 18, 18, 10, 10, 16, 16, 16, 16, 16, 16, 16, 10] 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460868382 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460868382 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460868382/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460868382/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460868382 Building ZINC001460868382 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460868382' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460868382 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460868382 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460868382/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460868382 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 80) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/80: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3c(Br)c(F)cc(F)c32)cc1Cl) `ZINC001460868382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460868382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460868382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001460868382 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3c(Br)c(F)cc(F)c32)cc1Cl NO_LONG_NAME dock atom 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', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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, 5, 5, 5, 1, 1, 17, 1, 15, 1, 1, 15, 1, 1, 1, 16, 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] 0 hydrogens 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, 2, 10, 10, 1, 1, 1, 3, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 10, 18, 18, 18, 10, 10, 17, 17, 17, 17, 17, 17, 17, 10] 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460868382 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460868382/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460868382 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 81) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/81: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3c(Br)c(F)cc(F)c32)cc1Cl) `ZINC001460868382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460868382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460868382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001460868382 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3c(Br)c(F)cc(F)c32)cc1Cl NO_LONG_NAME dock atom 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', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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, 5, 5, 5, 1, 1, 17, 1, 15, 1, 1, 15, 1, 1, 1, 16, 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] 0 hydrogens 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, 2, 10, 10, 1, 1, 1, 3, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 10, 10, 10, 18, 18, 18, 10, 10, 16, 16, 16, 16, 16, 16, 16, 10] 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460868382 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460868382 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460868382/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460868382/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460868382 Building ZINC001460901183 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460901183' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460901183 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460901183 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460901183/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460901183 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/82 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/82' -> `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)c1ccc(C)cc1F) `ZINC001460901183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460901183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460901183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001460901183 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)c1ccc(C)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', '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, 5, 1, 1, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 5, 5, 5, 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]) total number of confs: 57 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460901183 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460901183/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460901183 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 83) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/83 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/83' -> `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)c1ccc(C)cc1F) `ZINC001460901183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460901183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460901183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001460901183 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)c1ccc(C)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', '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, 5, 1, 1, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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] 0 hydrogens need rotated 50 conformations in 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, 10, 10, 10, 10, 3, 3, 3, 13, 13, 6, 13, 3, 3, 3, 5, 5, 5, 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]) total number of confs: 59 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460901183 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460901183 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460901183/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460901183/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460901183 Building ZINC001460901183 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460901183' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460901183 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460901183 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460901183/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460901183 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 82) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)c1ccc(C)cc1F) `ZINC001460901183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460901183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460901183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001460901183 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)c1ccc(C)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', '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, 5, 1, 1, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 5, 5, 5, 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]) total number of confs: 57 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460901183 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460901183/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460901183 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 83) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)c1ccc(C)cc1F) `ZINC001460901183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460901183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460901183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001460901183 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)c1ccc(C)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', '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, 5, 1, 1, 1, 1, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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] 0 hydrogens need rotated 50 conformations in 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, 10, 10, 10, 10, 3, 3, 3, 13, 13, 6, 13, 3, 3, 3, 5, 5, 5, 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]) total number of confs: 59 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460901183 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001460901183 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460901183/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460901183/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001460901183 Building ZINC001461084153 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461084153' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461084153 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461084153 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461084153/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461084153 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/84 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/84' -> `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)N1CCCc2c1cccc2C(F)(F)F) `ZINC001461084153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461084153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461084153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001461084153 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCc2c1cccc2C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 1, 1, 1, 3, 8, 13, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16] 40 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 60 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461084153 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461084153/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461084153 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 85) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/85 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/85' -> `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)N1CCCc2c1cccc2C(F)(F)F) `ZINC001461084153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461084153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461084153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001461084153 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCc2c1cccc2C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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: [4, 4, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 1, 1, 1, 3, 8, 13, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16] 45 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 64 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461084153 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001461084153 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461084153/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461084153/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461084153 Building ZINC001461084153 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461084153' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461084153 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461084153 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461084153/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461084153 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 84) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/84: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCc2c1cccc2C(F)(F)F) `ZINC001461084153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461084153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461084153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001461084153 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCc2c1cccc2C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 1, 1, 1, 3, 8, 13, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16] 40 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 60 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461084153 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461084153/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461084153 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 85) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/85: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCc2c1cccc2C(F)(F)F) `ZINC001461084153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461084153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461084153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001461084153 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCc2c1cccc2C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 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: [4, 4, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 1, 1, 1, 3, 8, 13, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16] 45 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 64 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461084153 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001461084153 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461084153/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461084153/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461084153 Building ZINC001461156717 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461156717' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461156717 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461156717 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461156717/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461156717 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/86 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(COc3ccc(F)cc3)cc2)cc1Cl) `ZINC001461156717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461156717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461156717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001461156717 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(COc3ccc(F)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', '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, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 9, 9, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 9, 9, 22, 22, 22, 22, 22, 22, 9, 9, 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: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461156717 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461156717/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461156717 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 87) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/87 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/87' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(COc3ccc(F)cc3)cc2)cc1Cl) `ZINC001461156717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461156717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461156717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001461156717 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(COc3ccc(F)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', '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, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 7, 9, 29, 29, 29, 29, 29, 29, 29, 29, 9, 9, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 9, 9, 29, 29, 29, 29, 29, 29, 9, 9, 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: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461156717 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001461156717 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461156717/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461156717/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461156717 Building ZINC001461156717 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461156717' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461156717 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461156717 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461156717/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461156717 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 86) grep: /scratch/xiaobo/12845/xbi-8058088.35/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)NCc2ccc(COc3ccc(F)cc3)cc2)cc1Cl) `ZINC001461156717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461156717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461156717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001461156717 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(COc3ccc(F)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', '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, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 9, 9, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 9, 9, 22, 22, 22, 22, 22, 22, 9, 9, 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: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461156717 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461156717/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461156717 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 87) grep: /scratch/xiaobo/12845/xbi-8058088.35/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)NCc2ccc(COc3ccc(F)cc3)cc2)cc1Cl) `ZINC001461156717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461156717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461156717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001461156717 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(COc3ccc(F)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', '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, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 7, 9, 29, 29, 29, 29, 29, 29, 29, 29, 9, 9, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 9, 9, 29, 29, 29, 29, 29, 29, 9, 9, 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: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461156717 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001461156717 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461156717/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461156717/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461156717 Building ZINC001461227625 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461227625' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461227625 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461227625 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461227625/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461227625 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/88 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCC2(c3cccc(OC(F)(F)F)c3)CCC2)cc1Cl) `ZINC001461227625.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461227625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461227625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001461227625 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCC2(c3cccc(OC(F)(F)F)c3)CCC2)cc1Cl NO_LONG_NAME dock atom 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', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 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] 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: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8, 29, 30, 30, 30, 8, 5, 5, 5, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 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: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461227625 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461227625/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461227625 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 89) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/89 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/89' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCC2(c3cccc(OC(F)(F)F)c3)CCC2)cc1Cl) `ZINC001461227625.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461227625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461227625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001461227625 none COc1ccc([C@]([O-])([SiH3])C(=O)NCC2(c3cccc(OC(F)(F)F)c3)CCC2)cc1Cl NO_LONG_NAME dock atom 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', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 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] 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: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 6, 9, 9, 9, 9, 9, 31, 31, 31, 31, 9, 6, 6, 6, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 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: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461227625 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001461227625 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461227625/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461227625/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461227625 Building ZINC001461227625 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461227625' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461227625 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461227625 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461227625/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461227625 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 88) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/88: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCC2(c3cccc(OC(F)(F)F)c3)CCC2)cc1Cl) `ZINC001461227625.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461227625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461227625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001461227625 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCC2(c3cccc(OC(F)(F)F)c3)CCC2)cc1Cl NO_LONG_NAME dock atom 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', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 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] 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: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8, 29, 30, 30, 30, 8, 5, 5, 5, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 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: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461227625 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461227625/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461227625 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 89) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/89: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCC2(c3cccc(OC(F)(F)F)c3)CCC2)cc1Cl) `ZINC001461227625.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461227625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461227625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001461227625 none COc1ccc([C@]([O-])([SiH3])C(=O)NCC2(c3cccc(OC(F)(F)F)c3)CCC2)cc1Cl NO_LONG_NAME dock atom 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', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 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] 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: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 6, 9, 9, 9, 9, 9, 31, 31, 31, 31, 9, 6, 6, 6, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 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: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461227625 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001461227625 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461227625/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461227625/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461227625 Building ZINC001461229768 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461229768' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461229768 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461229768 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461229768/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461229768 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/90 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/90' -> `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)NCCCc1c(Cl)cccc1Cl) `ZINC001461229768.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461229768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461229768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001461229768 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCc1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', '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'] 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, 16, 1, 1, 1, 1, 16, 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] 0 hydrogens need rotated 50 conformations in 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, 16, 29, 34, 34, 34, 34, 34, 34, 34, 34, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 16, 16, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 184 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461229768 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461229768/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461229768 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 91) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/91 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/91' -> `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)NCCCc1c(Cl)cccc1Cl) `ZINC001461229768.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461229768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461229768/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001461229768 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCc1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', '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'] 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, 16, 1, 1, 1, 1, 16, 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] 0 hydrogens need rotated 50 conformations in 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, 16, 29, 34, 34, 34, 34, 34, 34, 34, 34, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 3, 16, 16, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 192 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461229768 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001461229768 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461229768/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461229768/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461229768 Building ZINC001461229768 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461229768' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461229768 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461229768 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461229768/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461229768 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 90) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCc1c(Cl)cccc1Cl) `ZINC001461229768.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461229768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461229768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001461229768 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCc1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', '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'] 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, 16, 1, 1, 1, 1, 16, 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] 0 hydrogens need rotated 50 conformations in 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, 16, 29, 34, 34, 34, 34, 34, 34, 34, 34, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 16, 16, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 184 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461229768 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461229768/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461229768 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 91) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCc1c(Cl)cccc1Cl) `ZINC001461229768.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461229768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461229768/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001461229768 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCc1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', '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'] 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, 16, 1, 1, 1, 1, 16, 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] 0 hydrogens need rotated 50 conformations in 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, 16, 29, 34, 34, 34, 34, 34, 34, 34, 34, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 3, 16, 16, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 192 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461229768 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001461229768 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461229768/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461229768/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461229768 Building ZINC001461360051 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461360051' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461360051 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461360051 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461360051/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461360051 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/92 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccccc1C) `ZINC001461360051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461360051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461360051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001461360051 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 13, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 2, 9, 9, 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: 59 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461360051 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461360051/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461360051 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 93) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/93 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/93' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccccc1C) `ZINC001461360051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461360051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461360051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001461360051 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 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, 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: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461360051 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001461360051 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461360051/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461360051/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461360051 Building ZINC001461360051 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461360051' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461360051 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461360051 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461360051/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461360051 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 92) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/92: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccccc1C) `ZINC001461360051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461360051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461360051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001461360051 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 13, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 2, 9, 9, 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: 59 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461360051 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461360051/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461360051 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 93) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/93: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccccc1C) `ZINC001461360051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461360051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461360051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001461360051 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 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, 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: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461360051 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001461360051 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461360051/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461360051/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461360051 Building ZINC001461456861 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461456861' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461456861 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461456861 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461456861/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461456861 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/94 `/scratch/xiaobo/12845/xbi-8058088.35/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)Nc1nc(Br)cc2ccccc21) `ZINC001461456861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461456861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461456861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001461456861 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc(Br)cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 17, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 4, 5, 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]) total number of confs: 66 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461456861 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461456861/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461456861 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 95) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/95 `/scratch/xiaobo/12845/xbi-8058088.35/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)Nc1nc(Br)cc2ccccc21) `ZINC001461456861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461456861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461456861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001461456861 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc(Br)cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 17, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 12, 12, 7, 12, 12, 4, 4, 4, 5, 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]) total number of confs: 71 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461456861 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001461456861 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461456861/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461456861/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461456861 Building ZINC001461456861 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461456861' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461456861 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461456861 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461456861/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461456861 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 94) grep: /scratch/xiaobo/12845/xbi-8058088.35/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)Nc1nc(Br)cc2ccccc21) `ZINC001461456861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461456861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461456861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001461456861 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc(Br)cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 17, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 4, 5, 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]) total number of confs: 66 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461456861 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461456861/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461456861 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 95) grep: /scratch/xiaobo/12845/xbi-8058088.35/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)Nc1nc(Br)cc2ccccc21) `ZINC001461456861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461456861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461456861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001461456861 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc(Br)cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 17, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 12, 12, 7, 12, 12, 4, 4, 4, 5, 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]) total number of confs: 71 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461456861 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001461456861 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461456861/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461456861/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461456861 Building ZINC001461491666 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491666' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491666 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461491666 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491666/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491666 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/96 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/96' -> `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)c2ccccc2)cc1) `ZINC001461491666.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461491666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001461491666 none COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c2ccccc2)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', '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, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 29, 29, 8, 4, 8, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 8, 16, 16, 8, 16, 16, 29, 29, 29, 29, 29, 29, 29, 4, 9, 9, 16, 16, 8, 16, 16, 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: 156 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491666 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491666/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491666 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 97) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/97 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/97' -> `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)c2ccccc2)cc1) `ZINC001461491666.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461491666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491666/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001461491666 none COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c2ccccc2)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', '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, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 27, 27, 7, 4, 7, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 4, 7, 7, 13, 13, 13, 13, 13, 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]) total number of confs: 124 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491666 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001461491666 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491666/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491666/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491666 Building ZINC001461491666 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491666' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491666 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461491666 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491666/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491666 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 96) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c2ccccc2)cc1) `ZINC001461491666.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461491666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001461491666 none COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c2ccccc2)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', '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, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 29, 29, 8, 4, 8, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 8, 16, 16, 8, 16, 16, 29, 29, 29, 29, 29, 29, 29, 4, 9, 9, 16, 16, 8, 16, 16, 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: 156 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491666 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491666/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491666 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 97) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c2ccccc2)cc1) `ZINC001461491666.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461491666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491666/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001461491666 none COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c2ccccc2)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', '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, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 27, 27, 7, 4, 7, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 4, 7, 7, 13, 13, 13, 13, 13, 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]) total number of confs: 124 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491666 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001461491666 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491666/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491666/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491666 Building ZINC001461491673 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491673' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491673 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461491673 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491673/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491673 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/98 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/98' -> `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)c2ccccc2)cc1) `ZINC001461491673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461491673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001461491673 none COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c2ccccc2)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', '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, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 26, 26, 7, 4, 7, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 13, 13, 7, 13, 13, 26, 26, 26, 26, 26, 26, 26, 4, 7, 7, 13, 13, 7, 13, 13, 26, 26] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 135 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491673 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491673/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491673 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 99) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/99 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/99' -> `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)c2ccccc2)cc1) `ZINC001461491673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461491673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001461491673 none COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c2ccccc2)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', '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, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 29, 29, 8, 4, 8, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 8, 16, 16, 8, 16, 16, 29, 29, 29, 29, 29, 29, 29, 4, 9, 9, 16, 16, 8, 16, 16, 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: 156 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491673 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001461491673 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491673/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491673/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491673 Building ZINC001461491673 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491673' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491673 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461491673 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491673/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491673 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 98) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c2ccccc2)cc1) `ZINC001461491673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461491673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001461491673 none COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c2ccccc2)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', '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, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 26, 26, 7, 4, 7, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 13, 13, 7, 13, 13, 26, 26, 26, 26, 26, 26, 26, 4, 7, 7, 13, 13, 7, 13, 13, 26, 26] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 135 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491673 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491673/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491673 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 99) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c2ccccc2)cc1) `ZINC001461491673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461491673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001461491673 none COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c2ccccc2)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', '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, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 29, 29, 8, 4, 8, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 8, 16, 16, 8, 16, 16, 29, 29, 29, 29, 29, 29, 29, 4, 9, 9, 16, 16, 8, 16, 16, 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: 156 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491673 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001461491673 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491673/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491673/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461491673 Building ZINC001461690594 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690594' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690594 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461690594 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690594/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690594 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/100 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCc3cc(NC(=O)OC(C)(C)C)ccc32)cc1Cl) `ZINC001461690594.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461690594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001461690594 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCc3cc(NC(=O)OC(C)(C)C)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', 'H', 'C.3', 'C.3', '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.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, 7, 5, 5, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 15, 21, 21, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 2, 4, 4, 4, 4, 4, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690594 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690594/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690594 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 101) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/101 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/101' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCc3cc(NC(=O)OC(C)(C)C)ccc32)cc1Cl) `ZINC001461690594.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461690594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690594/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001461690594 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCc3cc(NC(=O)OC(C)(C)C)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', 'H', 'C.3', 'C.3', '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.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, 7, 5, 5, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 5, 5, 5, 5, 5, 5, 5, 17, 23, 23, 24, 24, 24, 24, 5, 5, 5, 4, 4, 4, 8, 8, 8, 4, 4, 2, 5, 5, 5, 5, 5, 17, 24, 24, 24, 24, 24, 24, 24, 24, 24, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690594 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001461690594 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690594/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690594/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690594 Building ZINC001461690594 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690594' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690594 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461690594 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690594/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690594 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 100) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCc3cc(NC(=O)OC(C)(C)C)ccc32)cc1Cl) `ZINC001461690594.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461690594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001461690594 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCc3cc(NC(=O)OC(C)(C)C)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', 'H', 'C.3', 'C.3', '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.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, 7, 5, 5, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 15, 21, 21, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 2, 4, 4, 4, 4, 4, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690594 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690594/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690594 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 101) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCc3cc(NC(=O)OC(C)(C)C)ccc32)cc1Cl) `ZINC001461690594.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461690594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690594/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001461690594 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCc3cc(NC(=O)OC(C)(C)C)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', 'H', 'C.3', 'C.3', '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.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, 7, 5, 5, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 5, 5, 5, 5, 5, 5, 5, 17, 23, 23, 24, 24, 24, 24, 5, 5, 5, 4, 4, 4, 8, 8, 8, 4, 4, 2, 5, 5, 5, 5, 5, 17, 24, 24, 24, 24, 24, 24, 24, 24, 24, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690594 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001461690594 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690594/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690594/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690594 Building ZINC001461690599 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690599' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690599 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461690599 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690599/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690599 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/102 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCc3cc(NC(=O)OC(C)(C)C)ccc32)cc1Cl) `ZINC001461690599.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461690599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001461690599 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCc3cc(NC(=O)OC(C)(C)C)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', 'H', 'C.3', 'C.3', '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.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, 7, 5, 5, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 5, 5, 5, 5, 5, 5, 5, 18, 26, 26, 26, 26, 26, 26, 5, 5, 5, 4, 4, 4, 7, 7, 7, 4, 4, 2, 5, 5, 5, 5, 5, 18, 26, 26, 26, 26, 26, 26, 26, 26, 26, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690599 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690599/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690599 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 103) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/103 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/103' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCc3cc(NC(=O)OC(C)(C)C)ccc32)cc1Cl) `ZINC001461690599.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461690599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690599/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001461690599 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCc3cc(NC(=O)OC(C)(C)C)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', 'H', 'C.3', 'C.3', '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.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, 7, 5, 5, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 15, 22, 22, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 2, 4, 4, 4, 4, 4, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690599 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001461690599 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690599/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690599/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690599 Building ZINC001461690599 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690599' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690599 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461690599 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690599/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690599 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 102) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/102: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCc3cc(NC(=O)OC(C)(C)C)ccc32)cc1Cl) `ZINC001461690599.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461690599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001461690599 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCc3cc(NC(=O)OC(C)(C)C)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', 'H', 'C.3', 'C.3', '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.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, 7, 5, 5, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 5, 5, 5, 5, 5, 5, 5, 18, 26, 26, 26, 26, 26, 26, 5, 5, 5, 4, 4, 4, 7, 7, 7, 4, 4, 2, 5, 5, 5, 5, 5, 18, 26, 26, 26, 26, 26, 26, 26, 26, 26, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690599 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690599/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690599 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 103) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/103: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCc3cc(NC(=O)OC(C)(C)C)ccc32)cc1Cl) `ZINC001461690599.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461690599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690599/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001461690599 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCc3cc(NC(=O)OC(C)(C)C)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', 'H', 'C.3', 'C.3', '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.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, 7, 5, 5, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 15, 22, 22, 23, 23, 23, 23, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 2, 4, 4, 4, 4, 4, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690599 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001461690599 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690599/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690599/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461690599 Building ZINC001461772688 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461772688' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461772688 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461772688 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461772688/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461772688 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/104 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)ccc1NC(=O)OC(C)(C)C) `ZINC001461772688.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461772688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461772688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001461772688 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)ccc1NC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 3, 2, 18, 26, 29, 37, 37, 40, 37, 9, 9, 9, 9, 2, 6, 6, 9, 9, 19, 41, 37, 37, 43, 40, 40, 42, 36, 36] 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: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461772688 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461772688/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461772688 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 105) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/105 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/105' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)ccc1NC(=O)OC(C)(C)C) `ZINC001461772688.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461772688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461772688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001461772688 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)ccc1NC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 8, 9, 27, 36, 36, 43, 43, 43, 43, 9, 9, 9, 9, 2, 5, 5, 9, 9, 27, 43, 43, 43, 43, 43, 43, 43, 43, 43] 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: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461772688 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001461772688 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461772688/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461772688/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461772688 Building ZINC001461772688 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461772688' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461772688 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461772688 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461772688/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461772688 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 104) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)ccc1NC(=O)OC(C)(C)C) `ZINC001461772688.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461772688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461772688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001461772688 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)ccc1NC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 3, 2, 18, 26, 29, 37, 37, 40, 37, 9, 9, 9, 9, 2, 6, 6, 9, 9, 19, 41, 37, 37, 43, 40, 40, 42, 36, 36] 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: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461772688 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461772688/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461772688 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 105) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)ccc1NC(=O)OC(C)(C)C) `ZINC001461772688.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461772688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461772688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001461772688 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)ccc1NC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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, 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] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 8, 9, 27, 36, 36, 43, 43, 43, 43, 9, 9, 9, 9, 2, 5, 5, 9, 9, 27, 43, 43, 43, 43, 43, 43, 43, 43, 43] 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: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461772688 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001461772688 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461772688/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461772688/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461772688 Building ZINC001461969716 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461969716' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461969716 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461969716 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461969716/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461969716 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/106 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3c(s2)c(Br)ccc3F)cc1Cl) `ZINC001461969716.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461969716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461969716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001461969716 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3c(s2)c(Br)ccc3F)cc1Cl NO_LONG_NAME dock atom 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', 'S.3', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 14, 1, 17, 1, 1, 1, 15, 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: [22, 10, 2, 10, 10, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 22, 22, 22, 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: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461969716 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461969716/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461969716 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 107) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/107 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/107' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc3c(s2)c(Br)ccc3F)cc1Cl) `ZINC001461969716.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461969716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461969716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001461969716 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc3c(s2)c(Br)ccc3F)cc1Cl NO_LONG_NAME dock atom 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', 'S.3', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 14, 1, 17, 1, 1, 1, 15, 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: [22, 10, 2, 10, 10, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 22, 22, 22, 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: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461969716 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001461969716 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461969716/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461969716/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461969716 Building ZINC001461969716 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461969716' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461969716 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461969716 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461969716/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461969716 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 106) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3c(s2)c(Br)ccc3F)cc1Cl) `ZINC001461969716.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461969716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461969716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001461969716 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nc3c(s2)c(Br)ccc3F)cc1Cl NO_LONG_NAME dock atom 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', 'S.3', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 14, 1, 17, 1, 1, 1, 15, 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: [22, 10, 2, 10, 10, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 22, 22, 22, 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: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461969716 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461969716/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461969716 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 107) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc3c(s2)c(Br)ccc3F)cc1Cl) `ZINC001461969716.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461969716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461969716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001461969716 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nc3c(s2)c(Br)ccc3F)cc1Cl NO_LONG_NAME dock atom 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', 'S.3', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 14, 1, 17, 1, 1, 1, 15, 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: [22, 10, 2, 10, 10, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 22, 22, 22, 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: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461969716 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001461969716 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461969716/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461969716/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001461969716 Building ZINC001462017606 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462017606' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462017606 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462017606 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462017606/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462017606 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/108 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCc3cc(Br)c(Cl)cc32)cc1Cl) `ZINC001462017606.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462017606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462017606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001462017606 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCc3cc(Br)c(Cl)cc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 17, 1, 16, 1, 1, 1, 1, 16, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 2, 8, 8, 1, 1, 1, 2, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 8, 16, 16, 16, 8, 8, 13, 13, 13, 13, 13, 13, 8] 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462017606 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462017606/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462017606 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 109) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/109 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/109' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCc3cc(Br)c(Cl)cc32)cc1Cl) `ZINC001462017606.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462017606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462017606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001462017606 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCc3cc(Br)c(Cl)cc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 17, 1, 16, 1, 1, 1, 1, 16, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 2, 8, 8, 1, 1, 1, 2, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 8, 8, 8, 16, 16, 16, 8, 8, 12, 12, 12, 12, 12, 12, 8] 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462017606 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001462017606 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462017606/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462017606/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462017606 Building ZINC001462017606 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462017606' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462017606 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462017606 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462017606/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462017606 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 108) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCc3cc(Br)c(Cl)cc32)cc1Cl) `ZINC001462017606.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462017606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462017606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001462017606 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCc3cc(Br)c(Cl)cc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 17, 1, 16, 1, 1, 1, 1, 16, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 2, 8, 8, 1, 1, 1, 2, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 8, 16, 16, 16, 8, 8, 13, 13, 13, 13, 13, 13, 8] 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462017606 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462017606/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462017606 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 109) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCc3cc(Br)c(Cl)cc32)cc1Cl) `ZINC001462017606.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462017606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462017606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001462017606 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCc3cc(Br)c(Cl)cc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 17, 1, 16, 1, 1, 1, 1, 16, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 2, 8, 8, 1, 1, 1, 2, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 8, 8, 8, 16, 16, 16, 8, 8, 12, 12, 12, 12, 12, 12, 8] 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462017606 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001462017606 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462017606/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462017606/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462017606 Building ZINC001462076939 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076939' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076939 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462076939 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076939/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076939 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/110 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cc(Cl)ccc1C) `ZINC001462076939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462076939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001462076939 none COC[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cc(Cl)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'Br', 'S.3', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 16, 1, 1, 1, 5, 7, 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, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 14, 7, 14, 14, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 7, 11, 11, 11, 11, 11, 11, 11, 32, 32, 32, 27, 27, 14, 14, 14, 5, 5, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 139 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076939 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076939/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076939 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 111) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/111 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/111' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cc(Cl)ccc1C) `ZINC001462076939.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462076939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001462076939 none COC[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cc(Cl)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'Br', 'S.3', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 16, 1, 1, 1, 5, 7, 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, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 19, 10, 19, 19, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 10, 15, 15, 15, 15, 15, 15, 15, 31, 31, 31, 29, 29, 19, 19, 19, 5, 5, 15, 15, 15, 15, 15, 15] 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]) total number of confs: 135 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076939 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001462076939 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076939/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076939/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076939 Building ZINC001462076939 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076939' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076939 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462076939 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076939/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076939 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 110) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COC[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cc(Cl)ccc1C) `ZINC001462076939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462076939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001462076939 none COC[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cc(Cl)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'Br', 'S.3', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 16, 1, 1, 1, 5, 7, 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, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 14, 7, 14, 14, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 7, 11, 11, 11, 11, 11, 11, 11, 32, 32, 32, 27, 27, 14, 14, 14, 5, 5, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 139 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076939 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076939/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076939 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 111) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COC[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cc(Cl)ccc1C) `ZINC001462076939.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462076939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001462076939 none COC[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cc(Cl)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'Br', 'S.3', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 16, 1, 1, 1, 5, 7, 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, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 19, 10, 19, 19, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 10, 15, 15, 15, 15, 15, 15, 15, 31, 31, 31, 29, 29, 19, 19, 19, 5, 5, 15, 15, 15, 15, 15, 15] 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]) total number of confs: 135 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076939 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001462076939 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076939/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076939/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076939 Building ZINC001462076941 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076941' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076941 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462076941 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076941/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076941 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/112 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cc(Cl)ccc1C) `ZINC001462076941.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462076941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001462076941 none COC[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cc(Cl)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'Br', 'S.3', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 16, 1, 1, 1, 5, 7, 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, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 9, 19, 19, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 9, 14, 14, 14, 14, 14, 14, 14, 30, 30, 30, 28, 28, 19, 19, 19, 5, 5, 14, 14, 14, 14, 14, 14] 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]) total number of confs: 131 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076941 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076941/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076941 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 113) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/113 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/113' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](C)N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cc(Cl)ccc1C) `ZINC001462076941.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462076941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076941/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001462076941 none COC[C@H](C)N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cc(Cl)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'Br', 'S.3', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 16, 1, 1, 1, 5, 7, 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, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 13, 7, 13, 13, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 7, 11, 11, 11, 11, 11, 11, 11, 32, 32, 32, 28, 28, 13, 13, 13, 4, 4, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 139 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076941 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001462076941 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076941/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076941/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076941 Building ZINC001462076941 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076941' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076941 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462076941 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076941/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076941 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 112) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COC[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cc(Cl)ccc1C) `ZINC001462076941.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462076941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001462076941 none COC[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cc(Cl)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'Br', 'S.3', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 16, 1, 1, 1, 5, 7, 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, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 9, 19, 19, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 9, 14, 14, 14, 14, 14, 14, 14, 30, 30, 30, 28, 28, 19, 19, 19, 5, 5, 14, 14, 14, 14, 14, 14] 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]) total number of confs: 131 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076941 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076941/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076941 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 113) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COC[C@H](C)N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cc(Cl)ccc1C) `ZINC001462076941.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462076941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076941/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001462076941 none COC[C@H](C)N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cc(Cl)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'Br', 'S.3', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 16, 1, 1, 1, 5, 7, 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, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 13, 7, 13, 13, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 7, 11, 11, 11, 11, 11, 11, 11, 32, 32, 32, 28, 28, 13, 13, 13, 4, 4, 11, 11, 11, 11, 11, 11] 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]) total number of confs: 139 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076941 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001462076941 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076941/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076941/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462076941 Building ZINC001462107042 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107042' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107042 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462107042 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107042/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107042 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/114 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/114' -> `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@]1(Cc2ccccc2)C=CCCC1) `ZINC001462107042.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462107042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001462107042 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@]1(Cc2ccccc2)C=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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 31, 45, 45, 45, 45, 45, 45, 31, 31, 31, 31, 31, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 9, 9, 45, 45, 45, 45, 45, 45, 45, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 173 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107042 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107042/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107042 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 115) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/115 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/115' -> `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@]1(Cc2ccccc2)C=CCCC1) `ZINC001462107042.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462107042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001462107042 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@]1(Cc2ccccc2)C=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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 35, 46, 46, 46, 46, 46, 46, 35, 35, 35, 35, 35, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 10, 10, 46, 46, 46, 46, 46, 46, 46, 35, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 185 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107042 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001462107042 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107042/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107042/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107042 Building ZINC001462107042 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107042' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107042 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462107042 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107042/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107042 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 114) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/114: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@]1(Cc2ccccc2)C=CCCC1) `ZINC001462107042.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462107042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001462107042 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@]1(Cc2ccccc2)C=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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 31, 45, 45, 45, 45, 45, 45, 31, 31, 31, 31, 31, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 9, 9, 45, 45, 45, 45, 45, 45, 45, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 173 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107042 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107042/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107042 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 115) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/115: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@]1(Cc2ccccc2)C=CCCC1) `ZINC001462107042.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462107042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001462107042 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@]1(Cc2ccccc2)C=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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 35, 46, 46, 46, 46, 46, 46, 35, 35, 35, 35, 35, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 10, 10, 46, 46, 46, 46, 46, 46, 46, 35, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 185 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107042 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001462107042 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107042/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107042/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107042 Building ZINC001462107046 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107046' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107046 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462107046 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107046/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107046 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/116 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/116' -> `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@@]1(Cc2ccccc2)C=CCCC1) `ZINC001462107046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462107046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001462107046 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(Cc2ccccc2)C=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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 34, 46, 46, 46, 46, 46, 46, 34, 34, 34, 34, 34, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 10, 10, 46, 46, 46, 46, 46, 46, 46, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 179 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107046 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107046/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107046 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 117) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/117 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/117' -> `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@@]1(Cc2ccccc2)C=CCCC1) `ZINC001462107046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462107046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001462107046 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@]1(Cc2ccccc2)C=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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 32, 45, 45, 45, 45, 45, 45, 32, 32, 32, 32, 32, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 9, 9, 45, 45, 45, 45, 45, 45, 45, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 172 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107046 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001462107046 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107046/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107046/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107046 Building ZINC001462107046 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107046' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107046 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462107046 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107046/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107046 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 116) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/116: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(Cc2ccccc2)C=CCCC1) `ZINC001462107046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462107046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001462107046 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(Cc2ccccc2)C=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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 34, 46, 46, 46, 46, 46, 46, 34, 34, 34, 34, 34, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 10, 10, 46, 46, 46, 46, 46, 46, 46, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 179 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107046 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107046/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107046 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 117) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/117: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@]1(Cc2ccccc2)C=CCCC1) `ZINC001462107046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462107046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001462107046 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@]1(Cc2ccccc2)C=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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 32, 45, 45, 45, 45, 45, 45, 32, 32, 32, 32, 32, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 9, 9, 45, 45, 45, 45, 45, 45, 45, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 172 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107046 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001462107046 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107046/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107046/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462107046 Building ZINC001462489189 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462489189' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462489189 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462489189 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462489189/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462489189 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/118 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(Cl)cc1Oc1ccc(Cl)c(C)c1) `ZINC001462489189.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462489189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462489189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001462489189 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(Cl)cc1Oc1ccc(Cl)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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.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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 16, 1, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 12, 24, 24, 24, 24, 24, 24, 24, 28, 48, 48, 47, 48, 48, 48, 48, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 12, 12, 24, 24, 24, 48, 48, 48, 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, 48, 49, 50]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462489189 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462489189/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462489189 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 119) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/119 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/119' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(Cl)cc1Oc1ccc(Cl)c(C)c1) `ZINC001462489189.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462489189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462489189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001462489189 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(Cl)cc1Oc1ccc(Cl)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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.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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 16, 1, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 13, 26, 26, 19, 26, 26, 26, 26, 29, 49, 49, 49, 49, 49, 49, 49, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 26, 26, 26, 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]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462489189 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001462489189 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462489189/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462489189/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462489189 Building ZINC001462489189 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462489189' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462489189 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462489189 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462489189/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462489189 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 118) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(Cl)cc1Oc1ccc(Cl)c(C)c1) `ZINC001462489189.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462489189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462489189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001462489189 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(Cl)cc1Oc1ccc(Cl)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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.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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 16, 1, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 12, 24, 24, 24, 24, 24, 24, 24, 28, 48, 48, 47, 48, 48, 48, 48, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 12, 12, 24, 24, 24, 48, 48, 48, 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, 48, 49, 50]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462489189 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462489189/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462489189 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 119) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(Cl)cc1Oc1ccc(Cl)c(C)c1) `ZINC001462489189.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462489189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462489189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001462489189 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(Cl)cc1Oc1ccc(Cl)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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.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, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 16, 1, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 13, 26, 26, 19, 26, 26, 26, 26, 29, 49, 49, 49, 49, 49, 49, 49, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 26, 26, 26, 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]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462489189 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001462489189 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462489189/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462489189/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462489189 Building ZINC001462533296 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462533296' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462533296 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462533296 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462533296/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462533296 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/120 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc2cc(Br)ccc2o1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001462533296.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462533296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462533296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 34 natoms 33 natoms 32 natoms 31 names: ZINC001462533296 none O=C(NCc1cc2cc(Br)ccc2o1)[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.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 17, 1, 1, 1, 12, 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, 3, 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: [3, 1, 3, 3, 15, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 6, 6, 6, 6, 6, 3, 15, 15, 43, 43, 43, 43, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462533296 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462533296/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462533296 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 121) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/121 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/121' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc2cc(Br)ccc2o1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001462533296.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462533296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462533296/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 34 natoms 33 natoms 32 natoms 31 names: ZINC001462533296 none O=C(NCc1cc2cc(Br)ccc2o1)[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.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 17, 1, 1, 1, 12, 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, 3, 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: [3, 1, 3, 3, 15, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 6, 6, 6, 6, 6, 3, 15, 15, 43, 43, 43, 43, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462533296 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001462533296 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462533296/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462533296/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462533296 Building ZINC001462533296 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462533296' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462533296 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462533296 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462533296/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462533296 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 120) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(NCc1cc2cc(Br)ccc2o1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001462533296.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462533296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462533296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 34 natoms 33 natoms 32 natoms 31 names: ZINC001462533296 none O=C(NCc1cc2cc(Br)ccc2o1)[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.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 17, 1, 1, 1, 12, 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, 3, 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: [3, 1, 3, 3, 15, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 6, 6, 6, 6, 6, 3, 15, 15, 43, 43, 43, 43, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462533296 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462533296/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462533296 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 121) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(NCc1cc2cc(Br)ccc2o1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001462533296.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462533296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462533296/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 34 natoms 33 natoms 32 natoms 31 names: ZINC001462533296 none O=C(NCc1cc2cc(Br)ccc2o1)[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.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 17, 1, 1, 1, 12, 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, 3, 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: [3, 1, 3, 3, 15, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 6, 6, 6, 6, 6, 3, 15, 15, 43, 43, 43, 43, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462533296 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001462533296 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462533296/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462533296/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462533296 Building ZINC001462624906 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001462624906 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/122 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccccc1)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CCCCC1) `ZINC001462624906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462624906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001462624906 none CN(Cc1ccccc1)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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.2', 'C.2', 'C.2', 'C.2', 'Br', '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'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 39, 39, 39, 19, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 39, 39, 39, 39, 39, 16, 16, 3, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 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]) total number of confs: 123 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 123) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/123 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/123' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccccc1)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CCCCC1) `ZINC001462624906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462624906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001462624906 none CN(Cc1ccccc1)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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.2', 'C.2', 'C.2', 'C.2', 'Br', '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'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 39, 39, 39, 19, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 39, 39, 39, 39, 39, 16, 16, 3, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 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]) total number of confs: 123 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 124) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/124 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/124' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccccc1)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CCCCC1) `ZINC001462624906.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001462624906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001462624906 none CN(Cc1ccccc1)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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.2', 'C.2', 'C.2', 'C.2', 'Br', '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'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 36, 36, 36, 36, 36, 17, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 26, 26, 36, 36, 36, 36, 36, 14, 14, 3, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 114 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 125) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/125 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/125' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccccc1)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CCCCC1) `ZINC001462624906.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001462624906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001462624906 none CN(Cc1ccccc1)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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.2', 'C.2', 'C.2', 'C.2', 'Br', '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'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 36, 36, 36, 36, 36, 17, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 26, 26, 36, 36, 36, 36, 36, 14, 14, 3, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 114 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001462624906 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 Building ZINC001462624906 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001462624906 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 122) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CN(Cc1ccccc1)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CCCCC1) `ZINC001462624906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462624906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001462624906 none CN(Cc1ccccc1)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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.2', 'C.2', 'C.2', 'C.2', 'Br', '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'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 39, 39, 39, 19, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 39, 39, 39, 39, 39, 16, 16, 3, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 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]) total number of confs: 123 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 123) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CN(Cc1ccccc1)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CCCCC1) `ZINC001462624906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462624906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001462624906 none CN(Cc1ccccc1)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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.2', 'C.2', 'C.2', 'C.2', 'Br', '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'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 39, 39, 39, 19, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 39, 39, 39, 39, 39, 16, 16, 3, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 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]) total number of confs: 123 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 124) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/124: 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(Cc1ccccc1)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CCCCC1) `ZINC001462624906.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001462624906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001462624906 none CN(Cc1ccccc1)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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.2', 'C.2', 'C.2', 'C.2', 'Br', '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'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 36, 36, 36, 36, 36, 17, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 26, 26, 36, 36, 36, 36, 36, 14, 14, 3, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 114 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 125) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/125: 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(Cc1ccccc1)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CCCCC1) `ZINC001462624906.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001462624906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001462624906 none CN(Cc1ccccc1)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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.2', 'C.2', 'C.2', 'C.2', 'Br', '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'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 36, 36, 36, 36, 36, 17, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 26, 26, 36, 36, 36, 36, 36, 14, 14, 3, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 114 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001462624906 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 Building ZINC001462624906 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001462624906 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 122) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CN(Cc1ccccc1)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CCCCC1) `ZINC001462624906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462624906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001462624906 none CN(Cc1ccccc1)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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.2', 'C.2', 'C.2', 'C.2', 'Br', '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'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 39, 39, 39, 19, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 39, 39, 39, 39, 39, 16, 16, 3, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 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]) total number of confs: 123 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 123) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CN(Cc1ccccc1)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CCCCC1) `ZINC001462624906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462624906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001462624906 none CN(Cc1ccccc1)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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.2', 'C.2', 'C.2', 'C.2', 'Br', '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'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 39, 39, 39, 19, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 39, 39, 39, 39, 39, 16, 16, 3, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 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]) total number of confs: 123 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 124) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/124: 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(Cc1ccccc1)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CCCCC1) `ZINC001462624906.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001462624906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001462624906 none CN(Cc1ccccc1)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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.2', 'C.2', 'C.2', 'C.2', 'Br', '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'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 36, 36, 36, 36, 36, 17, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 26, 26, 36, 36, 36, 36, 36, 14, 14, 3, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 114 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 125) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/125: 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(Cc1ccccc1)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CCCCC1) `ZINC001462624906.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001462624906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001462624906 none CN(Cc1ccccc1)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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.2', 'C.2', 'C.2', 'C.2', 'Br', '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'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 36, 36, 36, 36, 36, 17, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 26, 26, 36, 36, 36, 36, 36, 14, 14, 3, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 114 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001462624906 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 Building ZINC001462624906 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001462624906 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 122) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CN(Cc1ccccc1)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CCCCC1) `ZINC001462624906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462624906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001462624906 none CN(Cc1ccccc1)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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.2', 'C.2', 'C.2', 'C.2', 'Br', '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'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 39, 39, 39, 19, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 39, 39, 39, 39, 39, 16, 16, 3, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 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]) total number of confs: 123 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 123) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CN(Cc1ccccc1)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CCCCC1) `ZINC001462624906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462624906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001462624906 none CN(Cc1ccccc1)C1(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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.2', 'C.2', 'C.2', 'C.2', 'Br', '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'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 39, 39, 39, 19, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 39, 39, 39, 39, 39, 16, 16, 3, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 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]) total number of confs: 123 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 124) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/124: 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(Cc1ccccc1)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CCCCC1) `ZINC001462624906.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001462624906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001462624906 none CN(Cc1ccccc1)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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.2', 'C.2', 'C.2', 'C.2', 'Br', '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'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 36, 36, 36, 36, 36, 17, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 26, 26, 36, 36, 36, 36, 36, 14, 14, 3, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 114 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 125) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/125: 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(Cc1ccccc1)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CCCCC1) `ZINC001462624906.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001462624906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001462624906 none CN(Cc1ccccc1)C1(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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.2', 'C.2', 'C.2', 'C.2', 'Br', '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'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 36, 36, 36, 36, 36, 17, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 26, 26, 36, 36, 36, 36, 36, 14, 14, 3, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 114 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001462624906 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462624906 Building ZINC001462704892 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462704892' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462704892 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462704892 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462704892/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462704892 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/126 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/126' -> `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(C)cc2C)cn1) `ZINC001462704892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462704892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462704892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001462704892 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)Cc2ccc(Cl)cc2Oc2ccc(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.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', '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, 5, 5, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 5, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 9, 14, 14, 11, 14, 14, 14, 14, 27, 31, 31, 31, 31, 31, 31, 31, 4, 4, 7, 7, 7, 7, 7, 4, 5, 5, 5, 9, 9, 14, 14, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462704892 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462704892/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462704892 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 127) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/127 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/127' -> `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(C)cc2C)cn1) `ZINC001462704892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462704892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462704892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001462704892 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)Cc2ccc(Cl)cc2Oc2ccc(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.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', '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, 5, 5, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 5, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 9, 14, 14, 11, 14, 14, 14, 14, 26, 30, 30, 30, 30, 30, 30, 30, 4, 4, 7, 7, 7, 7, 7, 4, 5, 5, 5, 9, 9, 14, 14, 14, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462704892 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001462704892 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462704892/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462704892/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462704892 Building ZINC001462704892 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462704892' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462704892 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462704892 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462704892/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462704892 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 126) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)Cc2ccc(Cl)cc2Oc2ccc(C)cc2C)cn1) `ZINC001462704892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462704892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462704892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001462704892 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)Cc2ccc(Cl)cc2Oc2ccc(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.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', '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, 5, 5, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 5, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 9, 14, 14, 11, 14, 14, 14, 14, 27, 31, 31, 31, 31, 31, 31, 31, 4, 4, 7, 7, 7, 7, 7, 4, 5, 5, 5, 9, 9, 14, 14, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462704892 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462704892/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462704892 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 127) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)Cc2ccc(Cl)cc2Oc2ccc(C)cc2C)cn1) `ZINC001462704892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462704892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462704892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001462704892 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)Cc2ccc(Cl)cc2Oc2ccc(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.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', '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, 5, 5, 1, 1, 1, 1, 16, 1, 1, 12, 1, 1, 1, 1, 5, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 9, 14, 14, 11, 14, 14, 14, 14, 26, 30, 30, 30, 30, 30, 30, 30, 4, 4, 7, 7, 7, 7, 7, 4, 5, 5, 5, 9, 9, 14, 14, 14, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462704892 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001462704892 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462704892/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462704892/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462704892 Building ZINC001462706891 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462706891' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462706891 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462706891 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462706891/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462706891 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/128 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cc(Br)c3ccccc3c2)cc1Cl) `ZINC001462706891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462706891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462706891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001462706891 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cc(Br)c3ccccc3c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 7, 25, 25, 25, 25, 25, 25, 25, 25, 25, 23, 4, 4, 4, 6, 6, 6, 4, 4, 2, 7, 7, 25, 25, 25, 25, 25, 25, 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462706891 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462706891/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462706891 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 129) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/129 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/129' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cc(Br)c3ccccc3c2)cc1Cl) `ZINC001462706891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462706891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462706891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001462706891 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cc(Br)c3ccccc3c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 7, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 6, 6, 6, 4, 4, 2, 7, 7, 25, 25, 25, 25, 25, 25, 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462706891 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001462706891 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462706891/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462706891/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462706891 Building ZINC001462706891 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462706891' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462706891 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462706891 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462706891/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462706891 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 128) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cc(Br)c3ccccc3c2)cc1Cl) `ZINC001462706891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462706891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462706891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001462706891 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cc(Br)c3ccccc3c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 7, 25, 25, 25, 25, 25, 25, 25, 25, 25, 23, 4, 4, 4, 6, 6, 6, 4, 4, 2, 7, 7, 25, 25, 25, 25, 25, 25, 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462706891 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462706891/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462706891 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 129) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cc(Br)c3ccccc3c2)cc1Cl) `ZINC001462706891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462706891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462706891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001462706891 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cc(Br)c3ccccc3c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 7, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 6, 6, 6, 4, 4, 2, 7, 7, 25, 25, 25, 25, 25, 25, 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462706891 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001462706891 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462706891/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462706891/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462706891 Building ZINC001462813665 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462813665' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462813665 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462813665 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462813665/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462813665 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/130 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)scc1c1ccc(Cl)cc1) `ZINC001462813665.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462813665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462813665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001462813665 none NC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)scc1c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', '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', 'S.3', 'C.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'] dock atom type numbers: [8, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 14, 1, 1, 1, 1, 1, 1, 16, 1, 1, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 19, 25, 19, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 19, 19, 19, 19, 26, 26, 19, 19, 26, 26, 25, 25, 4, 8, 8, 19, 26, 26, 26, 26] 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]) total number of confs: 94 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462813665 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462813665/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462813665 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 131) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/131 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/131' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)scc1c1ccc(Cl)cc1) `ZINC001462813665.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462813665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462813665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001462813665 none NC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)scc1c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', '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', 'S.3', 'C.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'] dock atom type numbers: [8, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 14, 1, 1, 1, 1, 1, 1, 16, 1, 1, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 26, 20, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 20, 20, 20, 20, 27, 27, 27, 27, 27, 27, 26, 26, 4, 8, 8, 20, 27, 27, 27, 27] 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]) total number of confs: 74 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462813665 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001462813665 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462813665/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462813665/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462813665 Building ZINC001462813665 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462813665' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462813665 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462813665 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462813665/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462813665 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 130) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: NC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)scc1c1ccc(Cl)cc1) `ZINC001462813665.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462813665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462813665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001462813665 none NC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)scc1c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', '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', 'S.3', 'C.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'] dock atom type numbers: [8, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 14, 1, 1, 1, 1, 1, 1, 16, 1, 1, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 19, 25, 19, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 19, 19, 19, 19, 26, 26, 19, 19, 26, 26, 25, 25, 4, 8, 8, 19, 26, 26, 26, 26] 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]) total number of confs: 94 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462813665 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462813665/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462813665 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 131) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: NC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)scc1c1ccc(Cl)cc1) `ZINC001462813665.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462813665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462813665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001462813665 none NC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)scc1c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', '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', 'S.3', 'C.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'] dock atom type numbers: [8, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 14, 1, 1, 1, 1, 1, 1, 16, 1, 1, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 26, 20, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 20, 20, 20, 20, 27, 27, 27, 27, 27, 27, 26, 26, 4, 8, 8, 20, 27, 27, 27, 27] 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]) total number of confs: 74 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462813665 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001462813665 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462813665/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462813665/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462813665 Building ZINC001462832947 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462832947' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462832947 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462832947 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462832947/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462832947 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/132 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C)ccc1Oc1ccccc1CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001462832947.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462832947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462832947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001462832947 none COc1cc(C)ccc1Oc1ccccc1CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)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', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 5, 8, 5, 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, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 29, 29, 29, 29, 29, 28, 20, 20, 20, 20, 20, 20, 12, 5, 3, 5, 1, 3, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 5, 32, 32, 32, 29, 29, 29, 29, 29, 29, 20, 20, 20, 20, 12, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 60]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462832947 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462832947/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462832947 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 133) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/133 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/133' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C)ccc1Oc1ccccc1CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001462832947.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462832947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462832947/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001462832947 none COc1cc(C)ccc1Oc1ccccc1CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)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', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 5, 8, 5, 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, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 27, 19, 19, 19, 19, 19, 19, 12, 5, 3, 5, 1, 3, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 19, 19, 19, 19, 12, 12, 5, 5, 5, 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, 60]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462832947 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001462832947 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462832947/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462832947/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462832947 Building ZINC001462832947 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462832947' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462832947 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462832947 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462832947/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462832947 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 132) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1cc(C)ccc1Oc1ccccc1CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001462832947.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462832947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462832947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001462832947 none COc1cc(C)ccc1Oc1ccccc1CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)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', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 5, 8, 5, 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, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 29, 29, 29, 29, 29, 28, 20, 20, 20, 20, 20, 20, 12, 5, 3, 5, 1, 3, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 5, 32, 32, 32, 29, 29, 29, 29, 29, 29, 20, 20, 20, 20, 12, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 60]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462832947 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462832947/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462832947 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 133) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1cc(C)ccc1Oc1ccccc1CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001462832947.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462832947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462832947/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001462832947 none COc1cc(C)ccc1Oc1ccccc1CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)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', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', '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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 5, 8, 5, 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, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 27, 19, 19, 19, 19, 19, 19, 12, 5, 3, 5, 1, 3, 1, 1, 1, 4, 4, 4, 4, 6, 6, 6, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 19, 19, 19, 19, 12, 12, 5, 5, 5, 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, 60]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462832947 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001462832947 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462832947/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462832947/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462832947 Building ZINC001462885998 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462885998' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462885998 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462885998 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462885998/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462885998 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/134 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(C(C)C)c1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001462885998.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462885998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462885998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001462885998 none Cc1noc(C(C)C)c1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3] 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]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462885998 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462885998/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462885998 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 135) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/135 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/135' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(C(C)C)c1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001462885998.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462885998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462885998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001462885998 none Cc1noc(C(C)C)c1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3] 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]) total number of confs: 47 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462885998 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001462885998 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462885998/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462885998/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462885998 Building ZINC001462885998 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462885998' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462885998 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462885998 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462885998/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462885998 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 134) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1noc(C(C)C)c1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001462885998.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462885998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462885998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001462885998 none Cc1noc(C(C)C)c1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3] 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]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462885998 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462885998/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462885998 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 135) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1noc(C(C)C)c1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001462885998.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462885998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462885998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001462885998 none Cc1noc(C(C)C)c1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3] 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]) total number of confs: 47 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462885998 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001462885998 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462885998/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462885998/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462885998 Building ZINC001462896223 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462896223' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462896223 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462896223 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462896223/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462896223 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/136 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c(F)c(F)c1F) `ZINC001462896223.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462896223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462896223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001462896223 none CC(C)(C)OC(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c(F)c(F)c1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', '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', 'F', 'C.ar', 'F', 'C.ar', 'F', '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, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 15, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 41, 35, 26, 35, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 41, 41, 41, 41, 41, 41, 41, 41, 41, 26, 7, 3, 5, 5] 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: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462896223 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462896223/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462896223 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 137) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/137 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/137' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c(F)c(F)c1F) `ZINC001462896223.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462896223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462896223/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001462896223 none CC(C)(C)OC(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c(F)c(F)c1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', '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', 'F', 'C.ar', 'F', 'C.ar', 'F', '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, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 15, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 41, 35, 25, 35, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 41, 41, 41, 41, 41, 41, 41, 41, 41, 25, 7, 3, 5, 5] 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: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462896223 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001462896223 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462896223/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462896223/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462896223 Building ZINC001462896223 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462896223' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462896223 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462896223 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462896223/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462896223 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 136) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)OC(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c(F)c(F)c1F) `ZINC001462896223.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462896223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462896223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001462896223 none CC(C)(C)OC(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c(F)c(F)c1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', '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', 'F', 'C.ar', 'F', 'C.ar', 'F', '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, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 15, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 41, 35, 26, 35, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 41, 41, 41, 41, 41, 41, 41, 41, 41, 26, 7, 3, 5, 5] 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: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462896223 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462896223/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462896223 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 137) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)OC(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c(F)c(F)c1F) `ZINC001462896223.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462896223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462896223/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001462896223 none CC(C)(C)OC(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c(F)c(F)c1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', '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', 'F', 'C.ar', 'F', 'C.ar', 'F', '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, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 15, 1, 15, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 41, 35, 25, 35, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 41, 41, 41, 41, 41, 41, 41, 41, 41, 25, 7, 3, 5, 5] 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: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462896223 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001462896223 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462896223/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462896223/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462896223 Building ZINC001462990089 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462990089' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462990089 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462990089 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462990089/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462990089 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/138 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc(Br)cc1C(F)(F)F) `ZINC001462990089.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462990089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462990089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001462990089 none Cc1c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc(Br)cc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', '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', 'Br', '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'] dock atom type numbers: [5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 21, 21, 21, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 17, 17] 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462990089 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462990089/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462990089 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 139) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/139 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/139' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc(Br)cc1C(F)(F)F) `ZINC001462990089.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462990089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462990089/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001462990089 none Cc1c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc(Br)cc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', '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', 'Br', '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'] dock atom type numbers: [5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 4, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 19, 19, 19, 11, 15, 15, 15, 8, 15, 15, 15, 15, 15, 15, 15, 15, 4, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 11, 15, 13] 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462990089 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001462990089 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462990089/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462990089/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462990089 Building ZINC001462990089 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462990089' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462990089 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462990089 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462990089/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462990089 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 138) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc(Br)cc1C(F)(F)F) `ZINC001462990089.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462990089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462990089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001462990089 none Cc1c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc(Br)cc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', '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', 'Br', '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'] dock atom type numbers: [5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 21, 21, 21, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 17, 17] 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462990089 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462990089/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462990089 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 139) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc(Br)cc1C(F)(F)F) `ZINC001462990089.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462990089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462990089/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001462990089 none Cc1c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)cc(Br)cc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', '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', 'Br', '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'] dock atom type numbers: [5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 4, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 19, 19, 19, 11, 15, 15, 15, 8, 15, 15, 15, 15, 15, 15, 15, 15, 4, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 11, 15, 13] 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462990089 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001462990089 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462990089/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462990089/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001462990089 Building ZINC001463151898 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463151898' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463151898 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463151898 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463151898/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463151898 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/140 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Br)c(OCC(C)C)c2)cc1Cl) `ZINC001463151898.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463151898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463151898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001463151898 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Br)c(OCC(C)C)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 12, 5, 5, 5, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 6, 18, 22, 29, 29, 6, 4, 4, 4, 9, 9, 9, 4, 4, 2, 6, 6, 22, 22, 29, 29, 29, 29, 29, 29, 29, 6, 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463151898 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463151898/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463151898 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 141) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/141 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/141' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Br)c(OCC(C)C)c2)cc1Cl) `ZINC001463151898.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463151898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463151898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001463151898 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Br)c(OCC(C)C)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 12, 5, 5, 5, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 18, 21, 28, 29, 6, 4, 4, 4, 10, 10, 10, 4, 4, 2, 6, 6, 21, 21, 29, 29, 29, 29, 29, 29, 29, 6, 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463151898 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001463151898 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463151898/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463151898/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463151898 Building ZINC001463151898 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463151898' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463151898 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463151898 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463151898/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463151898 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 140) grep: /scratch/xiaobo/12845/xbi-8058088.35/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)Nc2ccc(Br)c(OCC(C)C)c2)cc1Cl) `ZINC001463151898.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463151898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463151898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001463151898 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Br)c(OCC(C)C)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 12, 5, 5, 5, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 6, 18, 22, 29, 29, 6, 4, 4, 4, 9, 9, 9, 4, 4, 2, 6, 6, 22, 22, 29, 29, 29, 29, 29, 29, 29, 6, 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463151898 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463151898/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463151898 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 141) grep: /scratch/xiaobo/12845/xbi-8058088.35/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)Nc2ccc(Br)c(OCC(C)C)c2)cc1Cl) `ZINC001463151898.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463151898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463151898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001463151898 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Br)c(OCC(C)C)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 12, 5, 5, 5, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 18, 21, 28, 29, 6, 4, 4, 4, 10, 10, 10, 4, 4, 2, 6, 6, 21, 21, 29, 29, 29, 29, 29, 29, 29, 6, 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463151898 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001463151898 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463151898/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463151898/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463151898 Building ZINC001463156652 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001463156652 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/142 `/scratch/xiaobo/12845/xbi-8058088.35/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)Nc1cc(F)ccc1[N@]1CC[C@H](C)CC1) `ZINC001463156652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463156652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001463156652 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(F)ccc1[N@]1CC[C@H](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 12, 12, 12, 10, 12, 12, 16, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 6, 12, 10, 12, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 143) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/143 `/scratch/xiaobo/12845/xbi-8058088.35/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)Nc1cc(F)ccc1[N@]1CC[C@H](C)CC1) `ZINC001463156652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463156652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001463156652 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(F)ccc1[N@]1CC[C@H](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 11, 11, 11, 9, 11, 11, 16, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 6, 11, 10, 11, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 144) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/144 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/144' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(F)ccc1[N@]1CC[C@@H](C)CC1) `ZINC001463156652.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001463156652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001463156652 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(F)ccc1[N@]1CC[C@@H](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 12, 12, 12, 12, 12, 12, 17, 37, 37, 37, 37, 37, 37, 37, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 6, 12, 12, 12, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 145) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/145 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/145' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(F)ccc1[N@]1CC[C@@H](C)CC1) `ZINC001463156652.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001463156652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001463156652 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(F)ccc1[N@]1CC[C@@H](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 8, 10, 10, 15, 32, 32, 32, 32, 32, 32, 32, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 5, 10, 8, 10, 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, 57, 58]) total number of confs: 74 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001463156652 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 Building ZINC001463156652 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001463156652 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 142) grep: /scratch/xiaobo/12845/xbi-8058088.35/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)Nc1cc(F)ccc1[N@]1CC[C@H](C)CC1) `ZINC001463156652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463156652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001463156652 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(F)ccc1[N@]1CC[C@H](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 12, 12, 12, 10, 12, 12, 16, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 6, 12, 10, 12, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 143) grep: /scratch/xiaobo/12845/xbi-8058088.35/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)Nc1cc(F)ccc1[N@]1CC[C@H](C)CC1) `ZINC001463156652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463156652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001463156652 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(F)ccc1[N@]1CC[C@H](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 11, 11, 11, 9, 11, 11, 16, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 6, 11, 10, 11, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 144) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/144: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(F)ccc1[N@]1CC[C@@H](C)CC1) `ZINC001463156652.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001463156652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001463156652 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(F)ccc1[N@]1CC[C@@H](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 12, 12, 12, 12, 12, 12, 17, 37, 37, 37, 37, 37, 37, 37, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 6, 12, 12, 12, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 145) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/145: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(F)ccc1[N@]1CC[C@@H](C)CC1) `ZINC001463156652.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001463156652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001463156652 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(F)ccc1[N@]1CC[C@@H](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 8, 10, 10, 15, 32, 32, 32, 32, 32, 32, 32, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 5, 10, 8, 10, 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, 57, 58]) total number of confs: 74 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001463156652 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 Building ZINC001463156652 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001463156652 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 142) grep: /scratch/xiaobo/12845/xbi-8058088.35/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)Nc1cc(F)ccc1[N@]1CC[C@H](C)CC1) `ZINC001463156652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463156652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001463156652 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(F)ccc1[N@]1CC[C@H](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 12, 12, 12, 10, 12, 12, 16, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 6, 12, 10, 12, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 143) grep: /scratch/xiaobo/12845/xbi-8058088.35/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)Nc1cc(F)ccc1[N@]1CC[C@H](C)CC1) `ZINC001463156652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463156652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001463156652 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(F)ccc1[N@]1CC[C@H](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 11, 11, 11, 9, 11, 11, 16, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 6, 11, 10, 11, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 144) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/144: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(F)ccc1[N@]1CC[C@@H](C)CC1) `ZINC001463156652.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001463156652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001463156652 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(F)ccc1[N@]1CC[C@@H](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 12, 12, 12, 12, 12, 12, 17, 37, 37, 37, 37, 37, 37, 37, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 6, 12, 12, 12, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 145) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/145: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(F)ccc1[N@]1CC[C@@H](C)CC1) `ZINC001463156652.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001463156652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001463156652 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(F)ccc1[N@]1CC[C@@H](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 8, 10, 10, 15, 32, 32, 32, 32, 32, 32, 32, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 5, 10, 8, 10, 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, 57, 58]) total number of confs: 74 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001463156652 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 Building ZINC001463156652 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001463156652 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 142) grep: /scratch/xiaobo/12845/xbi-8058088.35/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)Nc1cc(F)ccc1[N@]1CC[C@H](C)CC1) `ZINC001463156652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463156652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001463156652 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(F)ccc1[N@]1CC[C@H](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 12, 12, 12, 10, 12, 12, 16, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 6, 12, 10, 12, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 143) grep: /scratch/xiaobo/12845/xbi-8058088.35/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)Nc1cc(F)ccc1[N@]1CC[C@H](C)CC1) `ZINC001463156652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463156652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001463156652 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(F)ccc1[N@]1CC[C@H](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 11, 11, 11, 9, 11, 11, 16, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 6, 11, 10, 11, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 144) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/144: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(F)ccc1[N@]1CC[C@@H](C)CC1) `ZINC001463156652.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001463156652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001463156652 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(F)ccc1[N@]1CC[C@@H](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 12, 12, 12, 12, 12, 12, 17, 37, 37, 37, 37, 37, 37, 37, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 6, 12, 12, 12, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 145) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/145: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(F)ccc1[N@]1CC[C@@H](C)CC1) `ZINC001463156652.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001463156652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001463156652 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(F)ccc1[N@]1CC[C@@H](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 8, 10, 10, 15, 32, 32, 32, 32, 32, 32, 32, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 5, 10, 8, 10, 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, 57, 58]) total number of confs: 74 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001463156652 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463156652 Building ZINC001463162248 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463162248' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463162248 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463162248 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463162248/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463162248 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/146 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(OC(F)(F)F)ccc1Br)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001463162248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463162248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463162248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001463162248 none O=C(Nc1cc(OC(F)(F)F)ccc1Br)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 12, 5, 15, 15, 15, 1, 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, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 27, 27, 27, 27, 6, 6, 6, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 3, 6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463162248 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463162248/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463162248 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 147) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/147 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/147' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(OC(F)(F)F)ccc1Br)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001463162248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463162248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463162248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001463162248 none O=C(Nc1cc(OC(F)(F)F)ccc1Br)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 12, 5, 15, 15, 15, 1, 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, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 27, 27, 27, 27, 5, 5, 5, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 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, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463162248 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001463162248 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463162248/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463162248/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463162248 Building ZINC001463162248 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463162248' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463162248 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463162248 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463162248/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463162248 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 146) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1cc(OC(F)(F)F)ccc1Br)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001463162248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463162248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463162248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001463162248 none O=C(Nc1cc(OC(F)(F)F)ccc1Br)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 12, 5, 15, 15, 15, 1, 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, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 27, 27, 27, 27, 6, 6, 6, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 3, 6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463162248 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463162248/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463162248 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 147) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1cc(OC(F)(F)F)ccc1Br)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001463162248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463162248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463162248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001463162248 none O=C(Nc1cc(OC(F)(F)F)ccc1Br)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 12, 5, 15, 15, 15, 1, 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, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 27, 27, 27, 27, 5, 5, 5, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 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, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463162248 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001463162248 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463162248/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463162248/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463162248 Building ZINC001463227523 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463227523' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463227523 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463227523 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463227523/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463227523 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/148 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cc(Oc3cccc(Cl)c3)ccn2)cc1Cl) `ZINC001463227523.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463227523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463227523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001463227523 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cc(Oc3cccc(Cl)c3)ccn2)cc1Cl NO_LONG_NAME dock atom 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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.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, 5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 27, 31, 31, 31, 31, 31, 31, 13, 13, 13, 4, 4, 4, 8, 8, 8, 4, 4, 2, 9, 9, 13, 31, 31, 31, 31, 13, 13, 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463227523 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463227523/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463227523 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 149) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/149 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/149' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cc(Oc3cccc(Cl)c3)ccn2)cc1Cl) `ZINC001463227523.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463227523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463227523/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001463227523 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cc(Oc3cccc(Cl)c3)ccn2)cc1Cl NO_LONG_NAME dock atom 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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.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, 5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 8, 12, 12, 12, 26, 30, 30, 30, 30, 30, 30, 12, 12, 12, 4, 4, 4, 8, 8, 8, 4, 4, 2, 8, 8, 12, 30, 30, 30, 30, 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463227523 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001463227523 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463227523/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463227523/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463227523 Building ZINC001463227523 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463227523' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463227523 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463227523 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463227523/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463227523 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 148) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cc(Oc3cccc(Cl)c3)ccn2)cc1Cl) `ZINC001463227523.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463227523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463227523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001463227523 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cc(Oc3cccc(Cl)c3)ccn2)cc1Cl NO_LONG_NAME dock atom 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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.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, 5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 27, 31, 31, 31, 31, 31, 31, 13, 13, 13, 4, 4, 4, 8, 8, 8, 4, 4, 2, 9, 9, 13, 31, 31, 31, 31, 13, 13, 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463227523 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463227523/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463227523 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 149) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cc(Oc3cccc(Cl)c3)ccn2)cc1Cl) `ZINC001463227523.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463227523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463227523/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001463227523 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2cc(Oc3cccc(Cl)c3)ccn2)cc1Cl NO_LONG_NAME dock atom 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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.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, 5, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 1, 1, 8, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 8, 12, 12, 12, 26, 30, 30, 30, 30, 30, 30, 12, 12, 12, 4, 4, 4, 8, 8, 8, 4, 4, 2, 8, 8, 12, 30, 30, 30, 30, 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463227523 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001463227523 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463227523/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463227523/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463227523 Building ZINC001463398069 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398069' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398069 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463398069 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398069/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398069 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/150 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C(F)(F)F) `ZINC001463398069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463398069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463398069 none Cc1nn(c2ccccc2)c(C)c1[C@@H](CNC(=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', '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', '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, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 41, 41, 47, 47, 41, 47, 47, 41, 41, 39, 29, 39, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 39, 39, 39, 39, 41, 41, 41, 47, 47, 41, 47, 47, 41, 41, 41, 29, 29, 5, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 195 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398069 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398069/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398069 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 151) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/151 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/151' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C(F)(F)F) `ZINC001463398069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463398069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463398069 none Cc1nn(c2ccccc2)c(C)c1[C@@H](CNC(=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', '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', '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, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 41, 41, 49, 49, 41, 49, 49, 41, 41, 39, 27, 39, 6, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 39, 39, 39, 39, 41, 41, 41, 49, 49, 42, 49, 49, 41, 41, 41, 27, 27, 6, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 208 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398069 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001463398069 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398069/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398069/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398069 Building ZINC001463398069 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398069' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398069 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463398069 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398069/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398069 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 150) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/150: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C(F)(F)F) `ZINC001463398069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463398069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463398069 none Cc1nn(c2ccccc2)c(C)c1[C@@H](CNC(=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', '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', '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, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 41, 41, 47, 47, 41, 47, 47, 41, 41, 39, 29, 39, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 39, 39, 39, 39, 41, 41, 41, 47, 47, 41, 47, 47, 41, 41, 41, 29, 29, 5, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 195 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398069 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398069/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398069 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 151) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/151: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C(F)(F)F) `ZINC001463398069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463398069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463398069 none Cc1nn(c2ccccc2)c(C)c1[C@@H](CNC(=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', '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', '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, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 41, 41, 49, 49, 41, 49, 49, 41, 41, 39, 27, 39, 6, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 39, 39, 39, 39, 41, 41, 41, 49, 49, 42, 49, 49, 41, 41, 41, 27, 27, 6, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 208 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398069 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001463398069 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398069/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398069/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398069 Building ZINC001463398201 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398201' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463398201 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398201/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/152 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C(F)(F)F) `ZINC001463398201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463398201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463398201 none Cc1nn(c2ccccc2)c(C)c1[C@H](CNC(=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', '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', '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, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 49, 49, 49, 49, 49, 39, 39, 38, 27, 38, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 38, 38, 38, 38, 39, 39, 39, 49, 49, 49, 49, 49, 39, 39, 39, 27, 27, 6, 5, 5, 5, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 184 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398201/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 153) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/153 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/153' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C(F)(F)F) `ZINC001463398201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463398201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463398201 none Cc1nn(c2ccccc2)c(C)c1[C@H](CNC(=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', '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', '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, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 47, 47, 47, 47, 47, 40, 40, 38, 28, 38, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 38, 38, 38, 38, 40, 40, 40, 47, 47, 47, 47, 47, 40, 40, 40, 28, 28, 5, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 176 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001463398201 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398201/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398201/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398201 Building ZINC001463398201 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398201' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463398201 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398201/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 152) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C(F)(F)F) `ZINC001463398201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463398201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463398201 none Cc1nn(c2ccccc2)c(C)c1[C@H](CNC(=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', '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', '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, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 49, 49, 49, 49, 49, 39, 39, 38, 27, 38, 6, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 38, 38, 38, 38, 39, 39, 39, 49, 49, 49, 49, 49, 39, 39, 39, 27, 27, 6, 5, 5, 5, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 184 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398201/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 153) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C(F)(F)F) `ZINC001463398201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463398201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463398201 none Cc1nn(c2ccccc2)c(C)c1[C@H](CNC(=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', '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', '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, 5, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 47, 47, 47, 47, 47, 40, 40, 38, 28, 38, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 38, 38, 38, 38, 40, 40, 40, 47, 47, 47, 47, 47, 40, 40, 40, 28, 28, 5, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 176 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001463398201 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398201/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398201/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463398201 Building ZINC001463562074 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463562074' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463562074 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463562074 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463562074/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463562074 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/154 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C)c(S(=O)(=O)Nc3ccc(Cl)cc3)c2)cc1) `ZINC001463562074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463562074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463562074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001463562074 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C)c(S(=O)(=O)Nc3ccc(Cl)cc3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 17, 17, 4, 7, 17, 17, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 17, 3, 3, 3, 3, 3, 3, 3, 4, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 17, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 264 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463562074 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463562074/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463562074 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 155) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/155 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/155' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(C)c(S(=O)(=O)Nc3ccc(Cl)cc3)c2)cc1) `ZINC001463562074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463562074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463562074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001463562074 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(C)c(S(=O)(=O)Nc3ccc(Cl)cc3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 16, 16, 3, 11, 16, 16, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 16, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 16, 50, 50, 50, 50, 50, 16, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463562074 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001463562074 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463562074/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463562074/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463562074 Building ZINC001463562074 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463562074' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463562074 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463562074 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463562074/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463562074 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 154) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C)c(S(=O)(=O)Nc3ccc(Cl)cc3)c2)cc1) `ZINC001463562074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463562074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463562074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001463562074 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C)c(S(=O)(=O)Nc3ccc(Cl)cc3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 17, 17, 4, 7, 17, 17, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 17, 3, 3, 3, 3, 3, 3, 3, 4, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 17, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 264 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463562074 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463562074/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463562074 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 155) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(C)c(S(=O)(=O)Nc3ccc(Cl)cc3)c2)cc1) `ZINC001463562074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463562074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463562074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001463562074 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(C)c(S(=O)(=O)Nc3ccc(Cl)cc3)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 1, 14, 11, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 16, 16, 3, 11, 16, 16, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 16, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 16, 50, 50, 50, 50, 50, 16, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463562074 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001463562074 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463562074/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463562074/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463562074 Building ZINC001463573942 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463573942' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463573942 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463573942 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463573942/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463573942 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/156 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(NC(=O)c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2)cc1) `ZINC001463573942.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463573942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463573942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001463573942 none CCOc1ccc(NC(=O)c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 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: [40, 40, 35, 35, 35, 35, 15, 15, 3, 15, 3, 8, 8, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 35, 35, 40, 40, 40, 40, 40, 35, 35, 15, 8, 8, 3, 4, 4, 4, 4, 8, 8, 35, 35] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463573942 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463573942/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463573942 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 157) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/157 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/157' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(NC(=O)c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2)cc1) `ZINC001463573942.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463573942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463573942/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001463573942 none CCOc1ccc(NC(=O)c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 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: [35, 35, 31, 31, 31, 31, 15, 15, 5, 15, 3, 8, 8, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 31, 31, 35, 35, 35, 35, 35, 31, 31, 15, 8, 8, 3, 4, 4, 4, 4, 8, 8, 31, 31] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463573942 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001463573942 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463573942/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463573942/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463573942 Building ZINC001463573942 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463573942' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463573942 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463573942 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463573942/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463573942 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 156) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOc1ccc(NC(=O)c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2)cc1) `ZINC001463573942.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463573942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463573942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001463573942 none CCOc1ccc(NC(=O)c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 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: [40, 40, 35, 35, 35, 35, 15, 15, 3, 15, 3, 8, 8, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 35, 35, 40, 40, 40, 40, 40, 35, 35, 15, 8, 8, 3, 4, 4, 4, 4, 8, 8, 35, 35] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463573942 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463573942/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463573942 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 157) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOc1ccc(NC(=O)c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2)cc1) `ZINC001463573942.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463573942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463573942/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001463573942 none CCOc1ccc(NC(=O)c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 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: [35, 35, 31, 31, 31, 31, 15, 15, 5, 15, 3, 8, 8, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 31, 31, 35, 35, 35, 35, 35, 31, 31, 15, 8, 8, 3, 4, 4, 4, 4, 8, 8, 31, 31] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463573942 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001463573942 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463573942/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463573942/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463573942 Building ZINC001463794303 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001463794303 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/158 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@](Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001463794303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463794303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001463794303 none O=C(N[C@H]1CC[N@](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', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 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, 7, 7, 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] 0 hydrogens need rotated 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, 16, 16, 16, 16, 16, 36, 44, 44, 36, 40, 44, 44, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 16, 16, 16, 16, 36, 36, 44, 44, 44, 44, 16, 16, 16, 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, 41, 42, 43, 44, 45]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 159) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/159 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/159' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001463794303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463794303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001463794303 none O=C(N[C@H]1CC[N@@](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', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 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, 7, 7, 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] 0 hydrogens need rotated 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, 16, 16, 16, 16, 16, 36, 44, 44, 36, 40, 44, 44, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 16, 16, 16, 16, 36, 36, 44, 44, 44, 44, 16, 16, 16, 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, 41, 42, 43, 44, 45]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 160) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/160 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/160' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@](Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001463794303.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001463794303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001463794303 none O=C(N[C@H]1CC[N@](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', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 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, 7, 7, 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] 0 hydrogens need rotated 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, 16, 16, 16, 16, 16, 35, 44, 44, 35, 39, 44, 44, 16, 16, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 2, 16, 16, 16, 16, 35, 35, 44, 44, 44, 44, 16, 16, 16, 16, 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]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 161) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/161 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/161' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[N@@](Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001463794303.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001463794303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001463794303 none O=C(N[C@H]1CC[N@@](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', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 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, 7, 7, 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] 0 hydrogens need rotated 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, 16, 16, 16, 16, 16, 35, 44, 44, 35, 35, 44, 44, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 16, 16, 16, 16, 35, 35, 44, 44, 44, 44, 16, 16, 16, 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, 41, 42, 43, 44, 45]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001463794303 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 Building ZINC001463794303 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001463794303 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 158) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N[C@H]1CC[N@](Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001463794303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463794303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001463794303 none O=C(N[C@H]1CC[N@](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', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 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, 7, 7, 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] 0 hydrogens need rotated 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, 16, 16, 16, 16, 16, 36, 44, 44, 36, 40, 44, 44, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 16, 16, 16, 16, 36, 36, 44, 44, 44, 44, 16, 16, 16, 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, 41, 42, 43, 44, 45]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 159) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N[C@H]1CC[N@@](Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001463794303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463794303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001463794303 none O=C(N[C@H]1CC[N@@](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', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 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, 7, 7, 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] 0 hydrogens need rotated 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, 16, 16, 16, 16, 16, 36, 44, 44, 36, 40, 44, 44, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 16, 16, 16, 16, 36, 36, 44, 44, 44, 44, 16, 16, 16, 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, 41, 42, 43, 44, 45]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 160) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/160: 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@](Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001463794303.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001463794303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001463794303 none O=C(N[C@H]1CC[N@](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', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 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, 7, 7, 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] 0 hydrogens need rotated 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, 16, 16, 16, 16, 16, 35, 44, 44, 35, 39, 44, 44, 16, 16, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 2, 16, 16, 16, 16, 35, 35, 44, 44, 44, 44, 16, 16, 16, 16, 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]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 161) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/161: 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@@](Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001463794303.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001463794303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001463794303 none O=C(N[C@H]1CC[N@@](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', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 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, 7, 7, 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] 0 hydrogens need rotated 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, 16, 16, 16, 16, 16, 35, 44, 44, 35, 35, 44, 44, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 16, 16, 16, 16, 35, 35, 44, 44, 44, 44, 16, 16, 16, 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, 41, 42, 43, 44, 45]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001463794303 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 Building ZINC001463794303 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001463794303 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 158) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N[C@H]1CC[N@](Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001463794303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463794303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001463794303 none O=C(N[C@H]1CC[N@](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', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 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, 7, 7, 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] 0 hydrogens need rotated 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, 16, 16, 16, 16, 16, 36, 44, 44, 36, 40, 44, 44, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 16, 16, 16, 16, 36, 36, 44, 44, 44, 44, 16, 16, 16, 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, 41, 42, 43, 44, 45]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 159) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N[C@H]1CC[N@@](Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001463794303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463794303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001463794303 none O=C(N[C@H]1CC[N@@](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', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 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, 7, 7, 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] 0 hydrogens need rotated 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, 16, 16, 16, 16, 16, 36, 44, 44, 36, 40, 44, 44, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 16, 16, 16, 16, 36, 36, 44, 44, 44, 44, 16, 16, 16, 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, 41, 42, 43, 44, 45]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 160) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/160: 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@](Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001463794303.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001463794303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001463794303 none O=C(N[C@H]1CC[N@](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', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 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, 7, 7, 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] 0 hydrogens need rotated 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, 16, 16, 16, 16, 16, 35, 44, 44, 35, 39, 44, 44, 16, 16, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 2, 16, 16, 16, 16, 35, 35, 44, 44, 44, 44, 16, 16, 16, 16, 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]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 161) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/161: 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@@](Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001463794303.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001463794303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001463794303 none O=C(N[C@H]1CC[N@@](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', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 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, 7, 7, 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] 0 hydrogens need rotated 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, 16, 16, 16, 16, 16, 35, 44, 44, 35, 35, 44, 44, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 16, 16, 16, 16, 35, 35, 44, 44, 44, 44, 16, 16, 16, 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, 41, 42, 43, 44, 45]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001463794303 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 Building ZINC001463794303 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001463794303 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 158) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N[C@H]1CC[N@](Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001463794303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463794303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001463794303 none O=C(N[C@H]1CC[N@](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', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 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, 7, 7, 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] 0 hydrogens need rotated 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, 16, 16, 16, 16, 16, 36, 44, 44, 36, 40, 44, 44, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 16, 16, 16, 16, 36, 36, 44, 44, 44, 44, 16, 16, 16, 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, 41, 42, 43, 44, 45]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 159) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N[C@H]1CC[N@@](Cc2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001463794303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463794303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001463794303 none O=C(N[C@H]1CC[N@@](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', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 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, 7, 7, 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] 0 hydrogens need rotated 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, 16, 16, 16, 16, 16, 36, 44, 44, 36, 40, 44, 44, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 16, 16, 16, 16, 36, 36, 44, 44, 44, 44, 16, 16, 16, 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, 41, 42, 43, 44, 45]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 160) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/160: 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@](Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001463794303.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001463794303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001463794303 none O=C(N[C@H]1CC[N@](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', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 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, 7, 7, 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] 0 hydrogens need rotated 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, 16, 16, 16, 16, 16, 35, 44, 44, 35, 39, 44, 44, 16, 16, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 2, 16, 16, 16, 16, 35, 35, 44, 44, 44, 44, 16, 16, 16, 16, 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]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 161) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/161: 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@@](Cc2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001463794303.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001463794303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001463794303 none O=C(N[C@H]1CC[N@@](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', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 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, 7, 7, 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] 0 hydrogens need rotated 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, 16, 16, 16, 16, 16, 35, 44, 44, 35, 35, 44, 44, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 16, 16, 16, 16, 35, 35, 44, 44, 44, 44, 16, 16, 16, 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, 41, 42, 43, 44, 45]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001463794303 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463794303 Building ZINC001463802021 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463802021' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463802021 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463802021 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463802021/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463802021 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/162 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2ccc(C(F)(F)F)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001463802021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463802021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463802021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001463802021 none O=C(N1CCN(Cc2ccc(C(F)(F)F)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', 'N.3', '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', 'O.3', 'C.ar', '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, 5, 5, 10, 5, 1, 1, 1, 1, 5, 15, 15, 15, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 17, 17, 17, 17, 39, 45, 45, 39, 39, 45, 45, 45, 45, 45, 17, 17, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 39, 39, 45, 45, 45, 45, 17, 17, 17, 17, 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, 43, 44, 45]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463802021 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463802021/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463802021 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 163) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/163 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/163' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(Cc2ccc(C(F)(F)F)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001463802021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463802021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463802021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001463802021 none O=C(N1CCN(Cc2ccc(C(F)(F)F)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', 'N.3', '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', 'O.3', 'C.ar', '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, 5, 5, 10, 5, 1, 1, 1, 1, 5, 15, 15, 15, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 13, 13, 13, 13, 38, 47, 47, 40, 41, 47, 47, 47, 47, 47, 13, 13, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 13, 13, 13, 13, 38, 38, 47, 47, 47, 47, 13, 13, 13, 13, 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, 43, 44, 45]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463802021 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001463802021 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463802021/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463802021/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463802021 Building ZINC001463802021 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463802021' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463802021 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463802021 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463802021/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463802021 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 162) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CCN(Cc2ccc(C(F)(F)F)cc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001463802021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463802021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463802021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001463802021 none O=C(N1CCN(Cc2ccc(C(F)(F)F)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', 'N.3', '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', 'O.3', 'C.ar', '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, 5, 5, 10, 5, 1, 1, 1, 1, 5, 15, 15, 15, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 17, 17, 17, 17, 39, 45, 45, 39, 39, 45, 45, 45, 45, 45, 17, 17, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 17, 17, 17, 17, 39, 39, 45, 45, 45, 45, 17, 17, 17, 17, 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, 43, 44, 45]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463802021 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463802021/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463802021 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 163) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CCN(Cc2ccc(C(F)(F)F)cc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001463802021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463802021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463802021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001463802021 none O=C(N1CCN(Cc2ccc(C(F)(F)F)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', 'N.3', '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', 'O.3', 'C.ar', '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, 5, 5, 10, 5, 1, 1, 1, 1, 5, 15, 15, 15, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 13, 13, 13, 13, 38, 47, 47, 40, 41, 47, 47, 47, 47, 47, 13, 13, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 13, 13, 13, 13, 38, 38, 47, 47, 47, 47, 13, 13, 13, 13, 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, 43, 44, 45]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463802021 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001463802021 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463802021/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463802021/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463802021 Building ZINC001463914042 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914042' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914042 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463914042 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914042/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914042 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/164 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1Cl) `ZINC001463914042.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463914042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001463914042 none CCN(CC)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 30, 31, 37, 14, 30, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 30, 33, 33, 30, 33, 33, 33, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 14, 14, 4, 9, 9, 33, 33, 30, 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]) total number of confs: 226 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914042 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914042/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914042 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 165) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/165 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/165' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1Cl) `ZINC001463914042.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463914042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001463914042 none CCN(CC)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 29, 31, 37, 14, 29, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 29, 33, 33, 29, 33, 33, 33, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 14, 14, 4, 8, 8, 33, 33, 29, 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]) total number of confs: 228 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914042 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001463914042 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914042/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914042/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914042 Building ZINC001463914042 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914042' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914042 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463914042 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914042/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914042 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 164) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCN(CC)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1Cl) `ZINC001463914042.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463914042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001463914042 none CCN(CC)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 30, 31, 37, 14, 30, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 30, 33, 33, 30, 33, 33, 33, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 14, 14, 4, 9, 9, 33, 33, 30, 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]) total number of confs: 226 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914042 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914042/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914042 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 165) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCN(CC)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1Cl) `ZINC001463914042.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463914042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001463914042 none CCN(CC)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 29, 31, 37, 14, 29, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 29, 33, 33, 29, 33, 33, 33, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 14, 14, 4, 8, 8, 33, 33, 29, 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]) total number of confs: 228 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914042 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001463914042 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914042/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914042/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914042 Building ZINC001463914050 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914050' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914050 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463914050 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914050/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914050 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/166 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1Cl) `ZINC001463914050.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463914050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001463914050 none CCN(CC)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 27, 28, 34, 14, 27, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 27, 30, 30, 27, 30, 30, 30, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 14, 14, 4, 8, 8, 30, 30, 27, 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, 42, 43, 44]) total number of confs: 216 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914050 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914050/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914050 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 167) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/167 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/167' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1Cl) `ZINC001463914050.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463914050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914050/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001463914050 none CCN(CC)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 35, 13, 27, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 27, 30, 30, 30, 30, 30, 30, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 13, 13, 3, 9, 9, 30, 30, 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, 42, 43, 44]) total number of confs: 226 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914050 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001463914050 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914050/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914050/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914050 Building ZINC001463914050 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914050' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914050 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463914050 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914050/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914050 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 166) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCN(CC)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1Cl) `ZINC001463914050.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463914050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001463914050 none CCN(CC)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 27, 28, 34, 14, 27, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 27, 30, 30, 27, 30, 30, 30, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 14, 14, 4, 8, 8, 30, 30, 27, 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, 42, 43, 44]) total number of confs: 216 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914050 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914050/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914050 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 167) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCN(CC)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1Cl) `ZINC001463914050.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463914050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914050/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001463914050 none CCN(CC)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 35, 13, 27, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 27, 30, 30, 30, 30, 30, 30, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 13, 13, 3, 9, 9, 30, 30, 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, 42, 43, 44]) total number of confs: 226 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914050 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001463914050 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914050/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914050/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001463914050 Building ZINC001464142725 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464142725' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464142725 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464142725 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464142725/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464142725 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/168 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(CN(CCC)C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC) `ZINC001464142725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464142725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464142725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001464142725 none CCCOc1ccc(CN(CCC)C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', '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', '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, 5, 5, 12, 1, 1, 1, 1, 5, 8, 5, 5, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 24, 5, 5, 5, 5, 3, 2, 1, 2, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 11, 39, 39, 39, 39, 39, 35, 35, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 11, 11, 11] 50 rigid atoms, others: [9, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464142725 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464142725/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464142725 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 169) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/169 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/169' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(CN(CCC)C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC) `ZINC001464142725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464142725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464142725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001464142725 none CCCOc1ccc(CN(CCC)C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', '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', '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, 5, 5, 12, 1, 1, 1, 1, 5, 8, 5, 5, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 24, 5, 5, 5, 5, 3, 2, 1, 2, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 11, 39, 39, 39, 39, 39, 35, 35, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 11, 11, 11] 50 rigid atoms, others: [9, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464142725 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464142725 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464142725/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464142725/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464142725 Building ZINC001464142725 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464142725' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464142725 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464142725 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464142725/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464142725 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 168) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCCOc1ccc(CN(CCC)C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC) `ZINC001464142725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464142725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464142725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001464142725 none CCCOc1ccc(CN(CCC)C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', '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', '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, 5, 5, 12, 1, 1, 1, 1, 5, 8, 5, 5, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 24, 5, 5, 5, 5, 3, 2, 1, 2, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 11, 39, 39, 39, 39, 39, 35, 35, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 11, 11, 11] 50 rigid atoms, others: [9, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464142725 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464142725/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464142725 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 169) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCCOc1ccc(CN(CCC)C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC) `ZINC001464142725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464142725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464142725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001464142725 none CCCOc1ccc(CN(CCC)C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', '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', '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, 5, 5, 12, 1, 1, 1, 1, 5, 8, 5, 5, 5, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 24, 5, 5, 5, 5, 3, 2, 1, 2, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 11, 39, 39, 39, 39, 39, 35, 35, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 11, 11, 11] 50 rigid atoms, others: [9, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464142725 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464142725 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464142725/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464142725/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464142725 Building ZINC001464164742 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464164742' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464164742 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464164742 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464164742/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464164742 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/170 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C)c(Oc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cn2)c1) `ZINC001464164742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464164742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464164742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001464164742 none Cc1ccc(C)c(Oc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 8, 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, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 45, 16, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 6, 6, 1, 1, 1, 16, 50] 50 rigid atoms, others: [39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/12845/xbi-8058088.35/working/building/ZINC001464164742 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464164742/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464164742 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 171) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/171 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/171' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C)c(Oc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cn2)c1) `ZINC001464164742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464164742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464164742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001464164742 none Cc1ccc(C)c(Oc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 8, 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, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 44, 16, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 6, 6, 1, 1, 1, 16, 50] 50 rigid atoms, others: [39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464164742 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464164742 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464164742/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464164742/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464164742 Building ZINC001464164742 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464164742' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464164742 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464164742 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464164742/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464164742 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 170) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/170: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C)c(Oc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cn2)c1) `ZINC001464164742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464164742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464164742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001464164742 none Cc1ccc(C)c(Oc2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 8, 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, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 45, 16, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 6, 6, 1, 1, 1, 16, 50] 50 rigid atoms, others: [39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/12845/xbi-8058088.35/working/building/ZINC001464164742 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464164742/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464164742 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 171) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/171: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C)c(Oc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cn2)c1) `ZINC001464164742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464164742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464164742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001464164742 none Cc1ccc(C)c(Oc2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 8, 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, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 44, 16, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 6, 6, 1, 1, 1, 16, 50] 50 rigid atoms, others: [39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464164742 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464164742 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464164742/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464164742/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464164742 Building ZINC001464205865 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001464205865 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/172 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1) `ZINC001464205865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464205865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464205865 none CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 32, 32, 32, 32, 32, 24, 14, 24, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 46, 46, 46, 46, 46, 46, 46, 46, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 14, 14, 4, 3, 3, 6, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 32, 32] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 163 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 173) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/173 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/173' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1) `ZINC001464205865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464205865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464205865 none CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 35, 36, 35, 36, 36, 29, 15, 29, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 49, 49, 49, 49, 49, 49, 49, 49, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 15, 15, 3, 3, 3, 6, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 36, 36] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 185 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 174) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/174 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/174' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1) `ZINC001464205865.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001464205865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464205865 none CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 32, 32, 32, 32, 32, 24, 14, 24, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 46, 46, 46, 46, 46, 46, 46, 46, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 14, 14, 4, 3, 3, 6, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 32, 32] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 163 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 175) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/175 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/175' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1) `ZINC001464205865.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001464205865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464205865 none CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 35, 36, 35, 36, 36, 29, 15, 29, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 49, 49, 49, 49, 49, 49, 49, 49, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 15, 15, 3, 3, 3, 6, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 36, 36] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 185 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464205865 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 Building ZINC001464205865 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001464205865 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 172) grep: /scratch/xiaobo/12845/xbi-8058088.35/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)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1) `ZINC001464205865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464205865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464205865 none CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 32, 32, 32, 32, 32, 24, 14, 24, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 46, 46, 46, 46, 46, 46, 46, 46, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 14, 14, 4, 3, 3, 6, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 32, 32] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 163 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 173) grep: /scratch/xiaobo/12845/xbi-8058088.35/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)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1) `ZINC001464205865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464205865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464205865 none CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 35, 36, 35, 36, 36, 29, 15, 29, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 49, 49, 49, 49, 49, 49, 49, 49, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 15, 15, 3, 3, 3, 6, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 36, 36] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 185 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 174) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/174: 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)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1) `ZINC001464205865.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001464205865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464205865 none CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 32, 32, 32, 32, 32, 24, 14, 24, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 46, 46, 46, 46, 46, 46, 46, 46, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 14, 14, 4, 3, 3, 6, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 32, 32] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 163 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 175) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/175: 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)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1) `ZINC001464205865.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001464205865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464205865 none CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 35, 36, 35, 36, 36, 29, 15, 29, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 49, 49, 49, 49, 49, 49, 49, 49, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 15, 15, 3, 3, 3, 6, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 36, 36] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 185 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464205865 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 Building ZINC001464205865 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001464205865 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 172) grep: /scratch/xiaobo/12845/xbi-8058088.35/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)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1) `ZINC001464205865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464205865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464205865 none CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 32, 32, 32, 32, 32, 24, 14, 24, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 46, 46, 46, 46, 46, 46, 46, 46, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 14, 14, 4, 3, 3, 6, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 32, 32] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 163 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 173) grep: /scratch/xiaobo/12845/xbi-8058088.35/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)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1) `ZINC001464205865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464205865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464205865 none CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 35, 36, 35, 36, 36, 29, 15, 29, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 49, 49, 49, 49, 49, 49, 49, 49, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 15, 15, 3, 3, 3, 6, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 36, 36] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 185 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 174) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/174: 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)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1) `ZINC001464205865.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001464205865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464205865 none CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 32, 32, 32, 32, 32, 24, 14, 24, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 46, 46, 46, 46, 46, 46, 46, 46, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 14, 14, 4, 3, 3, 6, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 32, 32] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 163 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 175) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/175: 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)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1) `ZINC001464205865.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001464205865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464205865 none CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 35, 36, 35, 36, 36, 29, 15, 29, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 49, 49, 49, 49, 49, 49, 49, 49, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 15, 15, 3, 3, 3, 6, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 36, 36] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 185 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464205865 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 Building ZINC001464205865 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001464205865 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 172) grep: /scratch/xiaobo/12845/xbi-8058088.35/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)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1) `ZINC001464205865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464205865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464205865 none CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 32, 32, 32, 32, 32, 24, 14, 24, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 46, 46, 46, 46, 46, 46, 46, 46, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 14, 14, 4, 3, 3, 6, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 32, 32] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 163 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 173) grep: /scratch/xiaobo/12845/xbi-8058088.35/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)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1) `ZINC001464205865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464205865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464205865 none CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 35, 36, 35, 36, 36, 29, 15, 29, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 49, 49, 49, 49, 49, 49, 49, 49, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 15, 15, 3, 3, 3, 6, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 36, 36] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 185 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 174) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/174: 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)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1) `ZINC001464205865.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001464205865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464205865 none CC(C)c1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 32, 32, 32, 32, 32, 24, 14, 24, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 46, 46, 46, 46, 46, 46, 46, 46, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 14, 14, 4, 3, 3, 6, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 32, 32] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 163 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 175) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/175: 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)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1) `ZINC001464205865.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001464205865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464205865 none CC(C)c1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 35, 36, 35, 36, 36, 29, 15, 29, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 33, 49, 49, 49, 49, 49, 49, 49, 49, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 15, 15, 3, 3, 3, 6, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 36, 36] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 185 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464205865 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205865 Building ZINC001464205868 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001464205868 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/176 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1) `ZINC001464205868.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464205868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464205868 none CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 35, 36, 35, 36, 36, 30, 16, 30, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 34, 48, 48, 48, 48, 48, 48, 48, 48, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 16, 16, 3, 3, 3, 6, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 36, 36] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 184 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 177) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/177 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/177' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1) `ZINC001464205868.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464205868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464205868 none CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 31, 31, 31, 31, 31, 23, 13, 23, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 46, 46, 46, 46, 46, 46, 46, 46, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 13, 13, 3, 3, 3, 6, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 31, 31] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 164 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 178) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/178 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/178' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1) `ZINC001464205868.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001464205868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464205868 none CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 35, 36, 35, 36, 36, 30, 16, 30, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 34, 48, 48, 48, 48, 48, 48, 48, 48, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 16, 16, 3, 3, 3, 6, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 36, 36] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 184 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 179) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/179 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/179' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1) `ZINC001464205868.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001464205868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464205868 none CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 31, 31, 31, 31, 31, 23, 13, 23, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 46, 46, 46, 46, 46, 46, 46, 46, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 13, 13, 3, 3, 3, 6, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 31, 31] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 164 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464205868 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 Building ZINC001464205868 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001464205868 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 176) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1) `ZINC001464205868.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464205868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464205868 none CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 35, 36, 35, 36, 36, 30, 16, 30, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 34, 48, 48, 48, 48, 48, 48, 48, 48, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 16, 16, 3, 3, 3, 6, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 36, 36] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 184 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 177) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1) `ZINC001464205868.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464205868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464205868 none CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 31, 31, 31, 31, 31, 23, 13, 23, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 46, 46, 46, 46, 46, 46, 46, 46, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 13, 13, 3, 3, 3, 6, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 31, 31] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 164 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 178) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/178: 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)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1) `ZINC001464205868.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001464205868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464205868 none CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 35, 36, 35, 36, 36, 30, 16, 30, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 34, 48, 48, 48, 48, 48, 48, 48, 48, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 16, 16, 3, 3, 3, 6, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 36, 36] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 184 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 179) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/179: 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)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1) `ZINC001464205868.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001464205868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464205868 none CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 31, 31, 31, 31, 31, 23, 13, 23, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 46, 46, 46, 46, 46, 46, 46, 46, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 13, 13, 3, 3, 3, 6, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 31, 31] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 164 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464205868 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 Building ZINC001464205868 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001464205868 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 176) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1) `ZINC001464205868.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464205868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464205868 none CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 35, 36, 35, 36, 36, 30, 16, 30, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 34, 48, 48, 48, 48, 48, 48, 48, 48, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 16, 16, 3, 3, 3, 6, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 36, 36] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 184 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 177) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1) `ZINC001464205868.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464205868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464205868 none CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 31, 31, 31, 31, 31, 23, 13, 23, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 46, 46, 46, 46, 46, 46, 46, 46, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 13, 13, 3, 3, 3, 6, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 31, 31] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 164 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 178) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/178: 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)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1) `ZINC001464205868.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001464205868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464205868 none CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 35, 36, 35, 36, 36, 30, 16, 30, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 34, 48, 48, 48, 48, 48, 48, 48, 48, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 16, 16, 3, 3, 3, 6, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 36, 36] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 184 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 179) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/179: 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)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1) `ZINC001464205868.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001464205868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464205868 none CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 31, 31, 31, 31, 31, 23, 13, 23, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 46, 46, 46, 46, 46, 46, 46, 46, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 13, 13, 3, 3, 3, 6, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 31, 31] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 164 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464205868 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 Building ZINC001464205868 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001464205868 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 176) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1) `ZINC001464205868.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464205868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464205868 none CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 35, 36, 35, 36, 36, 30, 16, 30, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 34, 48, 48, 48, 48, 48, 48, 48, 48, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 16, 16, 3, 3, 3, 6, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 36, 36] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 184 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 177) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1) `ZINC001464205868.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464205868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464205868 none CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 31, 31, 31, 31, 31, 23, 13, 23, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 46, 46, 46, 46, 46, 46, 46, 46, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 13, 13, 3, 3, 3, 6, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 31, 31] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 164 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 178) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/178: 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)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1) `ZINC001464205868.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001464205868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464205868 none CC(C)c1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [36, 35, 36, 35, 36, 36, 30, 16, 30, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 34, 48, 48, 48, 48, 48, 48, 48, 48, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 16, 16, 3, 3, 3, 6, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 36, 36] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 184 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 179) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/179: 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)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1) `ZINC001464205868.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001464205868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464205868 none CC(C)c1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)N2CCc3sccc3C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 31, 31, 31, 31, 31, 23, 13, 23, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 46, 46, 46, 46, 46, 46, 46, 46, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 13, 13, 3, 3, 3, 6, 3, 3, 46, 46, 46, 46, 46, 46, 46, 46, 31, 31] 100 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 164 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464205868 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464205868 Building ZINC001464209915 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209915' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209915 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464209915 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209915/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209915 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/180 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCOc1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC) `ZINC001464209915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464209915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001464209915 none CCCCCOc1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC NO_LONG_NAME dock atom types: ['C.3', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 15, 5, 5, 5, 5, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 16, 16, 5, 5, 3, 3, 3, 2, 3, 3, 3, 3, 5, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 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/12845/xbi-8058088.35/working/building/ZINC001464209915 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209915/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209915 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 181) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/181 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/181' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCOc1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC) `ZINC001464209915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464209915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001464209915 none CCCCCOc1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC NO_LONG_NAME dock atom types: ['C.3', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 16, 14, 4, 4, 4, 4, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 8, 30, 30, 30, 30, 30, 30, 30, 30, 30, 16, 16, 4, 4, 3, 3, 3, 2, 2, 2, 2, 2, 4, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 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/12845/xbi-8058088.35/working/building/ZINC001464209915 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464209915 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209915/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209915/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209915 Building ZINC001464209915 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209915' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209915 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464209915 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209915/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209915 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 180) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCCCCOc1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC) `ZINC001464209915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464209915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001464209915 none CCCCCOc1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC NO_LONG_NAME dock atom types: ['C.3', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 15, 5, 5, 5, 5, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 16, 16, 5, 5, 3, 3, 3, 2, 3, 3, 3, 3, 5, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 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/12845/xbi-8058088.35/working/building/ZINC001464209915 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209915/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209915 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 181) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCCCCOc1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC) `ZINC001464209915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464209915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001464209915 none CCCCCOc1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC NO_LONG_NAME dock atom types: ['C.3', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 16, 14, 4, 4, 4, 4, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 8, 30, 30, 30, 30, 30, 30, 30, 30, 30, 16, 16, 4, 4, 3, 3, 3, 2, 2, 2, 2, 2, 4, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 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/12845/xbi-8058088.35/working/building/ZINC001464209915 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464209915 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209915/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209915/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209915 Building ZINC001464209922 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209922' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209922 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464209922 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209922/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209922 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/182 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCOc1ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC) `ZINC001464209922.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464209922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001464209922 none CCCCCOc1ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC NO_LONG_NAME dock atom types: ['C.3', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 16, 14, 4, 4, 4, 4, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 8, 30, 30, 30, 30, 30, 30, 30, 30, 30, 16, 16, 4, 4, 3, 3, 3, 2, 2, 2, 2, 2, 4, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 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/12845/xbi-8058088.35/working/building/ZINC001464209922 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209922/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209922 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 183) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/183 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/183' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCOc1ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC) `ZINC001464209922.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464209922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209922/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001464209922 none CCCCCOc1ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC NO_LONG_NAME dock atom types: ['C.3', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 16, 5, 5, 5, 5, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 17, 17, 5, 5, 3, 3, 3, 2, 3, 3, 3, 3, 5, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 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/12845/xbi-8058088.35/working/building/ZINC001464209922 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464209922 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209922/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209922/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209922 Building ZINC001464209922 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209922' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209922 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464209922 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209922/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209922 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 182) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCCCCOc1ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC) `ZINC001464209922.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464209922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001464209922 none CCCCCOc1ccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC NO_LONG_NAME dock atom types: ['C.3', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 16, 14, 4, 4, 4, 4, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 8, 30, 30, 30, 30, 30, 30, 30, 30, 30, 16, 16, 4, 4, 3, 3, 3, 2, 2, 2, 2, 2, 4, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 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/12845/xbi-8058088.35/working/building/ZINC001464209922 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209922/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209922 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 183) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCCCCOc1ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC) `ZINC001464209922.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464209922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209922/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001464209922 none CCCCCOc1ccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC NO_LONG_NAME dock atom types: ['C.3', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 16, 5, 5, 5, 5, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 17, 17, 5, 5, 3, 3, 3, 2, 3, 3, 3, 3, 5, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 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/12845/xbi-8058088.35/working/building/ZINC001464209922 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464209922 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209922/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209922/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464209922 Building ZINC001464282510 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464282510' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464282510 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464282510 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464282510/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464282510 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/184 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCCCc1cc(c2ccccc2)n[nH]1)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001464282510.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464282510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464282510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001464282510 none CN(CCCCCc1cc(c2ccccc2)n[nH]1)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens need 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, 3, 7, 9, 9, 11, 12, 30, 30, 30, 38, 38, 30, 38, 38, 30, 30, 30, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 7, 7, 9, 9, 9, 9, 11, 11, 12, 12, 30, 38, 38, 34, 38, 38, 4, 4, 4, 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464282510 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464282510/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464282510 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 185) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/185 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/185' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCCCc1cc(c2ccccc2)n[nH]1)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001464282510.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464282510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464282510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001464282510 none CN(CCCCCc1cc(c2ccccc2)n[nH]1)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens need 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, 3, 7, 8, 8, 10, 11, 30, 30, 30, 38, 38, 34, 38, 38, 30, 30, 30, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 7, 7, 8, 8, 8, 8, 10, 10, 11, 11, 30, 38, 38, 34, 38, 38, 4, 4, 4, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464282510 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464282510 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464282510/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464282510/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464282510 Building ZINC001464282510 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464282510' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464282510 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464282510 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464282510/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464282510 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 184) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CN(CCCCCc1cc(c2ccccc2)n[nH]1)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001464282510.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464282510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464282510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001464282510 none CN(CCCCCc1cc(c2ccccc2)n[nH]1)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens need 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, 3, 7, 9, 9, 11, 12, 30, 30, 30, 38, 38, 30, 38, 38, 30, 30, 30, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 7, 7, 9, 9, 9, 9, 11, 11, 12, 12, 30, 38, 38, 34, 38, 38, 4, 4, 4, 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464282510 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464282510/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464282510 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 185) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CN(CCCCCc1cc(c2ccccc2)n[nH]1)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001464282510.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464282510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464282510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001464282510 none CN(CCCCCc1cc(c2ccccc2)n[nH]1)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens need 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, 3, 7, 8, 8, 10, 11, 30, 30, 30, 38, 38, 34, 38, 38, 30, 30, 30, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 7, 7, 8, 8, 8, 8, 10, 10, 11, 11, 30, 38, 38, 34, 38, 38, 4, 4, 4, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464282510 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464282510 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464282510/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464282510/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464282510 Building ZINC001464391257 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464391257' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464391257 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464391257 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464391257/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464391257 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/186 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCCCC1)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1Cl) `ZINC001464391257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464391257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464391257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001464391257 none O=C(NC1CCCCC1)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', '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: [11, 1, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 16, 31, 31, 31, 31, 31, 7, 7, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 11, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 7, 3, 4, 4, 4, 4, 7, 7] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464391257 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464391257/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464391257 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 187) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/187 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/187' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCCCC1)c1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1Cl) `ZINC001464391257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464391257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464391257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001464391257 none O=C(NC1CCCCC1)c1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', '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: [11, 1, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 16, 31, 31, 31, 31, 31, 7, 7, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 11, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 7, 3, 4, 4, 4, 4, 7, 7] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464391257 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464391257 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464391257/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464391257/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464391257 Building ZINC001464391257 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464391257' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464391257 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464391257 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464391257/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464391257 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 186) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NC1CCCCC1)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1Cl) `ZINC001464391257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464391257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464391257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001464391257 none O=C(NC1CCCCC1)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', '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: [11, 1, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 16, 31, 31, 31, 31, 31, 7, 7, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 11, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 7, 3, 4, 4, 4, 4, 7, 7] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464391257 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464391257/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464391257 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 187) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NC1CCCCC1)c1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1Cl) `ZINC001464391257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464391257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464391257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001464391257 none O=C(NC1CCCCC1)c1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', '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: [11, 1, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 16, 31, 31, 31, 31, 31, 7, 7, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 11, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 7, 3, 4, 4, 4, 4, 7, 7] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464391257 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464391257 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464391257/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464391257/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464391257 Building ZINC001464503191 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503191' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503191 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464503191 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503191/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503191 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/188 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(C(F)(F)F)cc1) `ZINC001464503191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464503191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001464503191 none CCN(CC)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)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.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.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 12, 12, 12, 24, 8, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 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, 56, 57]) total number of confs: 203 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503191 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503191/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503191 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 189) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/189 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/189' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(C(F)(F)F)cc1) `ZINC001464503191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464503191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001464503191 none CCN(CC)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)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.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.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 14, 14, 14, 25, 9, 14, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 9, 9, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 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, 55, 56, 57]) total number of confs: 189 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503191 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464503191 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503191/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503191/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503191 Building ZINC001464503191 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503191' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503191 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464503191 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503191/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503191 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 188) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCN(CC)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(C(F)(F)F)cc1) `ZINC001464503191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464503191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001464503191 none CCN(CC)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)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.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.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 12, 12, 12, 24, 8, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 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, 56, 57]) total number of confs: 203 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503191 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503191/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503191 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 189) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCN(CC)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(C(F)(F)F)cc1) `ZINC001464503191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464503191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001464503191 none CCN(CC)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)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.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.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 14, 14, 14, 25, 9, 14, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 9, 9, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 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, 55, 56, 57]) total number of confs: 189 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503191 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464503191 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503191/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503191/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503191 Building ZINC001464503200 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503200' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464503200 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503200/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/190 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(C(F)(F)F)cc1) `ZINC001464503200.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464503200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001464503200 none CCN(CC)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)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.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.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 17, 17, 17, 27, 10, 17, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 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, 57]) total number of confs: 192 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503200/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 191) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/191 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/191' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(C(F)(F)F)cc1) `ZINC001464503200.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464503200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503200/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001464503200 none CCN(CC)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)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.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.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 13, 13, 13, 24, 9, 13, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 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, 56, 57]) total number of confs: 193 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464503200 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503200/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503200/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503200 Building ZINC001464503200 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503200' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464503200 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503200/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 190) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCN(CC)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(C(F)(F)F)cc1) `ZINC001464503200.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464503200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001464503200 none CCN(CC)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)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.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.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 17, 17, 17, 27, 10, 17, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 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, 57]) total number of confs: 192 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503200/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 191) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCN(CC)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1ccc(C(F)(F)F)cc1) `ZINC001464503200.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464503200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503200/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001464503200 none CCN(CC)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)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.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.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 13, 13, 13, 24, 9, 13, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 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, 56, 57]) total number of confs: 193 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464503200 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503200/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503200/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464503200 Building ZINC001464575132 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464575132' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464575132 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464575132 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464575132/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464575132 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/192 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCOc1ccc(Cl)cc1Cl)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001464575132.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464575132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464575132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001464575132 none O=C(NCCCOc1ccc(Cl)cc1Cl)[C@@]([O-])([SiH3])c1ccc(Br)s1 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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 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: [2, 1, 2, 2, 9, 10, 15, 40, 50, 50, 42, 50, 50, 50, 50, 1, 1, 1, 3, 3, 3, 3, 3, 2, 9, 9, 11, 11, 15, 14, 50, 50, 50, 3, 3] 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]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464575132 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464575132/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464575132 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 193) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/193 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/193' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCOc1ccc(Cl)cc1Cl)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001464575132.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464575132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464575132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001464575132 none O=C(NCCCOc1ccc(Cl)cc1Cl)[C@]([O-])([SiH3])c1ccc(Br)s1 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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 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: [2, 1, 2, 2, 9, 10, 15, 41, 50, 50, 47, 50, 50, 50, 50, 1, 1, 1, 3, 3, 3, 3, 3, 2, 9, 9, 11, 11, 14, 15, 50, 50, 50, 3, 3] 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464575132 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464575132 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464575132/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464575132/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464575132 Building ZINC001464575132 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464575132' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464575132 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464575132 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464575132/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464575132 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 192) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NCCCOc1ccc(Cl)cc1Cl)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001464575132.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464575132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464575132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001464575132 none O=C(NCCCOc1ccc(Cl)cc1Cl)[C@@]([O-])([SiH3])c1ccc(Br)s1 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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 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: [2, 1, 2, 2, 9, 10, 15, 40, 50, 50, 42, 50, 50, 50, 50, 1, 1, 1, 3, 3, 3, 3, 3, 2, 9, 9, 11, 11, 15, 14, 50, 50, 50, 3, 3] 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]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464575132 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464575132/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464575132 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 193) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NCCCOc1ccc(Cl)cc1Cl)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001464575132.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464575132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464575132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001464575132 none O=C(NCCCOc1ccc(Cl)cc1Cl)[C@]([O-])([SiH3])c1ccc(Br)s1 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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 1, 1, 1, 1, 16, 1, 1, 16, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 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: [2, 1, 2, 2, 9, 10, 15, 41, 50, 50, 47, 50, 50, 50, 50, 1, 1, 1, 3, 3, 3, 3, 3, 2, 9, 9, 11, 11, 14, 15, 50, 50, 50, 3, 3] 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464575132 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464575132 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464575132/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464575132/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464575132 Building ZINC001464633129 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633129' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633129 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464633129 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633129/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633129 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/194 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Br)cc1[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001464633129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464633129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001464633129 none COc1ccc(Br)cc1[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'H', 'C.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', 'H', 'H', '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, 7, 5, 5, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 10, 20, 20, 20, 10, 10, 10, 10, 10, 10, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 26, 20, 20, 20, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633129 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633129/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633129 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 195) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/195 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/195' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Br)cc1[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001464633129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464633129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001464633129 none COc1ccc(Br)cc1[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'H', 'C.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', 'H', 'H', '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, 7, 5, 5, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 24, 24, 24, 24, 13, 13, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 24, 24, 24, 13, 13, 13, 13, 13, 13, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633129 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464633129 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633129/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633129/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633129 Building ZINC001464633129 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633129' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633129 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464633129 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633129/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633129 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 194) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(Br)cc1[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001464633129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464633129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001464633129 none COc1ccc(Br)cc1[C@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'H', 'C.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', 'H', 'H', '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, 7, 5, 5, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 10, 20, 20, 20, 10, 10, 10, 10, 10, 10, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 26, 20, 20, 20, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633129 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633129/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633129 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 195) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(Br)cc1[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001464633129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464633129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001464633129 none COc1ccc(Br)cc1[C@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'H', 'C.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', 'H', 'H', '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, 7, 5, 5, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 24, 24, 24, 24, 13, 13, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 24, 24, 24, 13, 13, 13, 13, 13, 13, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633129 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464633129 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633129/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633129/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633129 Building ZINC001464633130 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633130' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633130 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464633130 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633130/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633130 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/196 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Br)cc1[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001464633130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464633130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001464633130 none COc1ccc(Br)cc1[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'H', 'C.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', 'H', 'H', '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, 7, 5, 5, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 24, 15, 24, 24, 24, 13, 13, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 24, 24, 24, 13, 13, 13, 13, 13, 13, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633130 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633130/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633130 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 197) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/197 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/197' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Br)cc1[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001464633130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464633130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001464633130 none COc1ccc(Br)cc1[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'H', 'C.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', 'H', 'H', '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, 7, 5, 5, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 13, 19, 19, 19, 9, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 19, 19, 19, 9, 9, 9, 9, 9, 9, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633130 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464633130 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633130/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633130/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633130 Building ZINC001464633130 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633130' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633130 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464633130 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633130/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633130 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 196) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/196: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Br)cc1[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001464633130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464633130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001464633130 none COc1ccc(Br)cc1[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'H', 'C.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', 'H', 'H', '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, 7, 5, 5, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 24, 15, 24, 24, 24, 13, 13, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 24, 24, 24, 13, 13, 13, 13, 13, 13, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633130 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633130/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633130 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 197) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/197: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Br)cc1[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001464633130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464633130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001464633130 none COc1ccc(Br)cc1[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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', 'H', 'C.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', 'H', 'H', '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, 7, 5, 5, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 13, 19, 19, 19, 9, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 19, 19, 19, 9, 9, 9, 9, 9, 9, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633130 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464633130 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633130/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633130/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464633130 Building ZINC001464694979 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694979' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694979 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464694979 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694979/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694979 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/198 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)NC[C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)C2)cc1) `ZINC001464694979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464694979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001464694979 none Cc1ccc(NC(=O)NC[C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)C2)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.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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 35, 34, 35, 15, 4, 4, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 4, 50, 50, 50, 50, 50, 50, 50, 47, 34, 15, 15, 4, 4, 4, 4, 4, 4, 2, 1, 2, 4, 4, 50, 50] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694979 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694979/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694979 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 199) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/199 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/199' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)NC[C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)C2)cc1) `ZINC001464694979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464694979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001464694979 none Cc1ccc(NC(=O)NC[C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)C2)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.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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 34, 31, 34, 11, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 50, 50, 50, 50, 50, 50, 50, 47, 31, 11, 11, 3, 3, 3, 3, 3, 3, 2, 1, 2, 3, 3, 50, 50] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694979 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464694979 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694979/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694979/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694979 Building ZINC001464694979 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694979' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694979 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464694979 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694979/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694979 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 198) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc(NC(=O)NC[C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)C2)cc1) `ZINC001464694979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464694979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001464694979 none Cc1ccc(NC(=O)NC[C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)C2)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.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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 35, 34, 35, 15, 4, 4, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 4, 50, 50, 50, 50, 50, 50, 50, 47, 34, 15, 15, 4, 4, 4, 4, 4, 4, 2, 1, 2, 4, 4, 50, 50] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694979 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694979/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694979 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 199) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc(NC(=O)NC[C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)C2)cc1) `ZINC001464694979.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464694979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001464694979 none Cc1ccc(NC(=O)NC[C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)C2)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.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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 34, 31, 34, 11, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 50, 50, 50, 50, 50, 50, 50, 47, 31, 11, 11, 3, 3, 3, 3, 3, 3, 2, 1, 2, 3, 3, 50, 50] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694979 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464694979 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694979/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694979/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694979 Building ZINC001464694987 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694987' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694987 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464694987 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694987/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694987 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/200 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)NC[C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)C2)cc1) `ZINC001464694987.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464694987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001464694987 none Cc1ccc(NC(=O)NC[C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)C2)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.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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 48, 34, 31, 34, 11, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 50, 50, 50, 50, 50, 50, 50, 48, 31, 11, 11, 3, 3, 3, 3, 3, 3, 2, 1, 2, 3, 3, 50, 50] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694987 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694987/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694987 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 201) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/201 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/201' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)NC[C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)C2)cc1) `ZINC001464694987.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464694987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001464694987 none Cc1ccc(NC(=O)NC[C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)C2)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.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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 36, 35, 36, 15, 4, 4, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 4, 50, 50, 50, 50, 50, 50, 50, 48, 35, 15, 15, 4, 4, 4, 4, 4, 4, 2, 1, 2, 4, 4, 50, 50] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694987 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464694987 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694987/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694987/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694987 Building ZINC001464694987 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694987' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694987 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464694987 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694987/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694987 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 200) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc(NC(=O)NC[C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)C2)cc1) `ZINC001464694987.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464694987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001464694987 none Cc1ccc(NC(=O)NC[C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)C2)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.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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 48, 34, 31, 34, 11, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 50, 50, 50, 50, 50, 50, 50, 48, 31, 11, 11, 3, 3, 3, 3, 3, 3, 2, 1, 2, 3, 3, 50, 50] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694987 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694987/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694987 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 201) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc(NC(=O)NC[C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)C2)cc1) `ZINC001464694987.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464694987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001464694987 none Cc1ccc(NC(=O)NC[C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)C2)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.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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 48, 36, 35, 36, 15, 4, 4, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 4, 50, 50, 50, 50, 50, 50, 50, 48, 35, 15, 15, 4, 4, 4, 4, 4, 4, 2, 1, 2, 4, 4, 50, 50] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694987 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464694987 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694987/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694987/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464694987 Building ZINC001464724799 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724799' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724799 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464724799 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724799/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724799 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/202 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CC[C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC) `ZINC001464724799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464724799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001464724799 none COc1ccc(CC[C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.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.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, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 5, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 30, 29, 29, 29, 17, 17, 10, 10, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 17, 30, 30, 30] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724799 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724799/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724799 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 203) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/203 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/203' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CC[C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC) `ZINC001464724799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464724799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001464724799 none COc1ccc(CC[C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.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.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, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 17, 8, 8, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 33, 32, 32, 32, 17, 17, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 17, 33, 33, 33] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724799 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464724799 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724799/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724799/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724799 Building ZINC001464724799 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724799' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724799 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464724799 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724799/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724799 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 202) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc(CC[C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC) `ZINC001464724799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464724799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001464724799 none COc1ccc(CC[C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.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.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, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 5, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 17, 30, 29, 29, 29, 17, 17, 10, 10, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 17, 30, 30, 30] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724799 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724799/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724799 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 203) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc(CC[C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC) `ZINC001464724799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464724799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001464724799 none COc1ccc(CC[C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.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.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, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 17, 8, 8, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 33, 32, 32, 32, 17, 17, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 17, 33, 33, 33] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724799 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464724799 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724799/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724799/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724799 Building ZINC001464724806 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724806' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724806 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464724806 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724806/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724806 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/204 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CC[C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC) `ZINC001464724806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464724806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001464724806 none COc1ccc(CC[C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.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.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, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 17, 8, 8, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 33, 32, 32, 32, 17, 17, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 17, 33, 33, 33] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724806 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724806/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724806 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 205) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/205 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/205' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CC[C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC) `ZINC001464724806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464724806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001464724806 none COc1ccc(CC[C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.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.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, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 19, 19, 19, 19, 10, 10, 5, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 30, 29, 29, 29, 19, 19, 10, 10, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 19, 30, 30, 30] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 99 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724806 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464724806 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724806/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724806/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724806 Building ZINC001464724806 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724806' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724806 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464724806 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724806/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724806 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 204) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc(CC[C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC) `ZINC001464724806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464724806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001464724806 none COc1ccc(CC[C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.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.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, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 17, 8, 8, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 33, 32, 32, 32, 17, 17, 8, 8, 8, 8, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 17, 33, 33, 33] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724806 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724806/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724806 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 205) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc(CC[C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC) `ZINC001464724806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464724806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001464724806 none COc1ccc(CC[C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.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.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, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 19, 19, 19, 19, 10, 10, 5, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 30, 29, 29, 29, 19, 19, 10, 10, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 19, 30, 30, 30] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 99 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724806 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464724806 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724806/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724806/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464724806 Building ZINC001464752689 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752689' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752689 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464752689 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752689/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752689 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/206 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccccc1) `ZINC001464752689.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464752689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001464752689 none C[C@H](NC(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 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, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 10, 22, 10, 7, 12, 7, 7, 7, 7, 7, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 22, 27, 27, 22, 27, 27, 22, 22, 22, 12, 7, 7, 7, 7, 4, 6, 6, 6, 6, 27, 27, 22, 27, 27] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 126 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752689 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752689/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752689 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 207) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/207 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/207' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccccc1) `ZINC001464752689.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464752689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752689/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001464752689 none C[C@H](NC(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 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, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 19, 10, 6, 11, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 19, 24, 24, 19, 24, 24, 19, 19, 19, 11, 6, 6, 6, 6, 3, 7, 7, 7, 7, 24, 24, 19, 24, 24] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 109 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752689 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464752689 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752689/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752689/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752689 Building ZINC001464752689 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752689' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752689 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464752689 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752689/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752689 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 206) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@H](NC(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccccc1) `ZINC001464752689.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464752689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001464752689 none C[C@H](NC(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 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, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 10, 22, 10, 7, 12, 7, 7, 7, 7, 7, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 22, 27, 27, 22, 27, 27, 22, 22, 22, 12, 7, 7, 7, 7, 4, 6, 6, 6, 6, 27, 27, 22, 27, 27] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 126 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752689 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752689/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752689 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 207) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@H](NC(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccccc1) `ZINC001464752689.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464752689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752689/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001464752689 none C[C@H](NC(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 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, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 19, 10, 6, 11, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 19, 24, 24, 19, 24, 24, 19, 19, 19, 11, 6, 6, 6, 6, 3, 7, 7, 7, 7, 24, 24, 19, 24, 24] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 109 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752689 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464752689 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752689/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752689/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752689 Building ZINC001464752692 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752692' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752692 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464752692 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752692/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752692 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/208 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccccc1) `ZINC001464752692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464752692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001464752692 none C[C@@H](NC(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 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, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 18, 10, 6, 11, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 18, 23, 23, 18, 23, 23, 18, 18, 18, 11, 6, 6, 6, 6, 3, 7, 7, 7, 7, 23, 23, 18, 23, 23] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 103 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752692 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752692/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752692 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 209) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/209 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/209' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccccc1) `ZINC001464752692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464752692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001464752692 none C[C@@H](NC(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 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, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 10, 22, 10, 7, 12, 7, 7, 7, 7, 7, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 22, 27, 27, 22, 27, 27, 22, 22, 22, 12, 7, 7, 7, 7, 4, 6, 6, 6, 6, 27, 27, 22, 27, 27] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 129 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752692 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464752692 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752692/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752692/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752692 Building ZINC001464752692 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752692' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752692 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464752692 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752692/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752692 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 208) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@@H](NC(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccccc1) `ZINC001464752692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464752692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001464752692 none C[C@@H](NC(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 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, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 18, 10, 6, 11, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 18, 23, 23, 18, 23, 23, 18, 18, 18, 11, 6, 6, 6, 6, 3, 7, 7, 7, 7, 23, 23, 18, 23, 23] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 103 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752692 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752692/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752692 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 209) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@@H](NC(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccccc1) `ZINC001464752692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464752692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001464752692 none C[C@@H](NC(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', '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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 1, 1, 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, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 10, 22, 10, 7, 12, 7, 7, 7, 7, 7, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 22, 27, 27, 22, 27, 27, 22, 22, 22, 12, 7, 7, 7, 7, 4, 6, 6, 6, 6, 27, 27, 22, 27, 27] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 129 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752692 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464752692 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752692/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752692/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464752692 Building ZINC001464795740 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464795740' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464795740 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464795740 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464795740/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464795740 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/210 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(C(c2ccc(Cl)cc2)c2ccc(Cl)cc2)CC1) `ZINC001464795740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464795740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464795740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001464795740 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(C(c2ccc(Cl)cc2)c2ccc(Cl)cc2)CC1 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.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 8, 21, 21, 21, 21, 34, 38, 38, 38, 38, 38, 38, 34, 38, 38, 34, 38, 38, 38, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 34, 38, 38, 38, 38, 38, 38, 38, 38, 21, 21, 21, 21] 38 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 132 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464795740 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464795740/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464795740 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 211) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/211 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/211' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(C(c2ccc(Cl)cc2)c2ccc(Cl)cc2)CC1) `ZINC001464795740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464795740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464795740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001464795740 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(C(c2ccc(Cl)cc2)c2ccc(Cl)cc2)CC1 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.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 2, 1, 1, 1, 4, 8, 19, 19, 19, 19, 42, 44, 44, 44, 44, 44, 44, 42, 44, 44, 42, 42, 44, 44, 19, 19, 2, 2, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 42, 44, 44, 44, 44, 44, 44, 44, 44, 19, 19, 19, 19] 44 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, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 158 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464795740 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464795740 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464795740/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464795740/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464795740 Building ZINC001464795740 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464795740' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464795740 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464795740 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464795740/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464795740 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 210) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/210: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(C(c2ccc(Cl)cc2)c2ccc(Cl)cc2)CC1) `ZINC001464795740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464795740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464795740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001464795740 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(C(c2ccc(Cl)cc2)c2ccc(Cl)cc2)CC1 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.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 8, 21, 21, 21, 21, 34, 38, 38, 38, 38, 38, 38, 34, 38, 38, 34, 38, 38, 38, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 34, 38, 38, 38, 38, 38, 38, 38, 38, 21, 21, 21, 21] 38 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 34, 37, 35, 36, 5, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 132 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464795740 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464795740/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464795740 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 211) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/211: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(C(c2ccc(Cl)cc2)c2ccc(Cl)cc2)CC1) `ZINC001464795740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464795740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464795740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001464795740 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(C(c2ccc(Cl)cc2)c2ccc(Cl)cc2)CC1 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.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 1, 1, 16, 1, 1, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 2, 1, 1, 1, 4, 8, 19, 19, 19, 19, 42, 44, 44, 44, 44, 44, 44, 42, 44, 44, 42, 42, 44, 44, 19, 19, 2, 2, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 42, 44, 44, 44, 44, 44, 44, 44, 44, 19, 19, 19, 19] 44 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, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 158 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464795740 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464795740 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464795740/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464795740/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464795740 Building ZINC001464844749 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464844749' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464844749 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464844749 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464844749/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464844749 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/212 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1nc(C2CCCCC2)cs1) `ZINC001464844749.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464844749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464844749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464844749 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1nc(C2CCCCC2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 5, 5, 5, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 11, 24, 24, 25, 49, 49, 49, 49, 49, 24, 24, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 10, 10, 11, 11, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464844749 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464844749/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464844749 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 213) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/213 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/213' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1nc(C2CCCCC2)cs1) `ZINC001464844749.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464844749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464844749/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464844749 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1nc(C2CCCCC2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 5, 5, 5, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 10, 22, 22, 23, 48, 48, 48, 48, 48, 22, 22, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 9, 9, 10, 10, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464844749 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464844749 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464844749/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464844749/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464844749 Building ZINC001464844749 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464844749' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464844749 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464844749 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464844749/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464844749 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 212) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1nc(C2CCCCC2)cs1) `ZINC001464844749.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464844749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464844749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464844749 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1nc(C2CCCCC2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 5, 5, 5, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 11, 24, 24, 25, 49, 49, 49, 49, 49, 24, 24, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 10, 10, 11, 11, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464844749 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464844749/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464844749 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 213) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1nc(C2CCCCC2)cs1) `ZINC001464844749.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464844749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464844749/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001464844749 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1nc(C2CCCCC2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 5, 5, 5, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 10, 22, 22, 23, 48, 48, 48, 48, 48, 22, 22, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 9, 9, 10, 10, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464844749 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001464844749 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464844749/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464844749/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001464844749 Building ZINC001465167729 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167729' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167729 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465167729 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167729/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167729 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/214 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)(CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)N[C@@H](C)c1ccccc1) `ZINC001465167729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465167729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 70 natoms 69 natoms 68 natoms 67 names: ZINC001465167729 none CCC(CC)(CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)N[C@@H](C)c1ccccc1 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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.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', '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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 10, 5, 7, 5, 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, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 9, 16, 17, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 16, 30, 30, 30, 30, 30, 30, 30, 30, 30, 18, 18, 18, 18, 18, 17, 17, 17, 17, 17, 9, 9, 2, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 30, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 152 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167729 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167729/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167729 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 215) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/215 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/215' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)(CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)N[C@@H](C)c1ccccc1) `ZINC001465167729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465167729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 70 natoms 69 natoms 68 natoms 67 names: ZINC001465167729 none CCC(CC)(CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)N[C@@H](C)c1ccccc1 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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.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', '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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 10, 5, 7, 5, 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, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 13, 15, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 9, 2, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 130 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167729 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001465167729 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167729/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167729/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167729 Building ZINC001465167729 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167729' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167729 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465167729 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167729/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167729 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 214) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCC(CC)(CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)N[C@@H](C)c1ccccc1) `ZINC001465167729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465167729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 70 natoms 69 natoms 68 natoms 67 names: ZINC001465167729 none CCC(CC)(CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)N[C@@H](C)c1ccccc1 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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.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', '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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 10, 5, 7, 5, 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, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 9, 16, 17, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 16, 30, 30, 30, 30, 30, 30, 30, 30, 30, 18, 18, 18, 18, 18, 17, 17, 17, 17, 17, 9, 9, 2, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 30, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 152 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167729 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167729/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167729 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 215) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCC(CC)(CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)N[C@@H](C)c1ccccc1) `ZINC001465167729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465167729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 70 natoms 69 natoms 68 natoms 67 names: ZINC001465167729 none CCC(CC)(CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)N[C@@H](C)c1ccccc1 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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.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', '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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 10, 5, 7, 5, 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, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 13, 15, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 9, 2, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 130 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167729 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001465167729 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167729/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167729/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167729 Building ZINC001465167730 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167730' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167730 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465167730 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167730/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167730 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/216 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)(CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)N[C@H](C)c1ccccc1) `ZINC001465167730.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465167730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 70 natoms 69 natoms 68 natoms 67 names: ZINC001465167730 none CCC(CC)(CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)N[C@H](C)c1ccccc1 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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.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', '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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 10, 5, 7, 5, 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, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 8, 19, 22, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 19, 39, 39, 39, 39, 39, 39, 39, 39, 39, 22, 22, 22, 21, 22, 22, 22, 22, 22, 22, 8, 8, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 190 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167730 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167730/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167730 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 217) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/217 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/217' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)(CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)N[C@H](C)c1ccccc1) `ZINC001465167730.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465167730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167730/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 70 natoms 69 natoms 68 natoms 67 names: ZINC001465167730 none CCC(CC)(CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)N[C@H](C)c1ccccc1 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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.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', '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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 10, 5, 7, 5, 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, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 9, 17, 19, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 18, 32, 32, 32, 32, 32, 32, 32, 32, 32, 20, 20, 20, 20, 20, 18, 19, 19, 19, 19, 9, 9, 2, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 32, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 166 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167730 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001465167730 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167730/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167730/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167730 Building ZINC001465167730 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167730' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167730 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465167730 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167730/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167730 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 216) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCC(CC)(CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)N[C@H](C)c1ccccc1) `ZINC001465167730.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465167730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 70 natoms 69 natoms 68 natoms 67 names: ZINC001465167730 none CCC(CC)(CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)N[C@H](C)c1ccccc1 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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.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', '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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 10, 5, 7, 5, 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, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 8, 19, 22, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 19, 39, 39, 39, 39, 39, 39, 39, 39, 39, 22, 22, 22, 21, 22, 22, 22, 22, 22, 22, 8, 8, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 190 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167730 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167730/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167730 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 217) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCC(CC)(CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)N[C@H](C)c1ccccc1) `ZINC001465167730.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465167730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167730/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 70 natoms 69 natoms 68 natoms 67 names: ZINC001465167730 none CCC(CC)(CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)N[C@H](C)c1ccccc1 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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.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', '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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 10, 5, 7, 5, 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, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 9, 17, 19, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 18, 32, 32, 32, 32, 32, 32, 32, 32, 32, 20, 20, 20, 20, 20, 18, 19, 19, 19, 19, 9, 9, 2, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 32, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 166 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167730 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001465167730 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167730/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167730/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465167730 Building ZINC001465326548 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326548' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326548 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465326548 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326548/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326548 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/218 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](Cc3cc(Cl)ccc3OC)C2)cc1Cl) `ZINC001465326548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465326548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001465326548 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](Cc3cc(Cl)ccc3OC)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', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 16, 1, 1, 1, 12, 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] 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] 0 hydrogens 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, 2, 4, 4, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 8, 20, 20, 20, 14, 20, 20, 20, 26, 3, 4, 4, 4, 11, 11, 11, 4, 4, 3, 3, 3, 3, 3, 3, 8, 8, 20, 20, 20, 26, 26, 26, 3, 3, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326548 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326548/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326548 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 219) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/219 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/219' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](Cc3cc(Cl)ccc3OC)C2)cc1Cl) `ZINC001465326548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465326548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001465326548 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](Cc3cc(Cl)ccc3OC)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', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 16, 1, 1, 1, 12, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 2, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 10, 22, 22, 22, 16, 22, 22, 22, 30, 3, 2, 2, 2, 6, 6, 6, 2, 2, 3, 3, 3, 3, 3, 3, 10, 10, 22, 22, 22, 30, 30, 30, 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326548 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001465326548 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326548/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326548/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326548 Building ZINC001465326548 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326548' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326548 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465326548 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326548/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326548 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 218) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/218: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](Cc3cc(Cl)ccc3OC)C2)cc1Cl) `ZINC001465326548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465326548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001465326548 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](Cc3cc(Cl)ccc3OC)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', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 16, 1, 1, 1, 12, 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] 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] 0 hydrogens 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, 2, 4, 4, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 8, 20, 20, 20, 14, 20, 20, 20, 26, 3, 4, 4, 4, 11, 11, 11, 4, 4, 3, 3, 3, 3, 3, 3, 8, 8, 20, 20, 20, 26, 26, 26, 3, 3, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326548 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326548/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326548 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 219) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/219: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](Cc3cc(Cl)ccc3OC)C2)cc1Cl) `ZINC001465326548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465326548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001465326548 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](Cc3cc(Cl)ccc3OC)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', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 16, 1, 1, 1, 12, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 2, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 10, 22, 22, 22, 16, 22, 22, 22, 30, 3, 2, 2, 2, 6, 6, 6, 2, 2, 3, 3, 3, 3, 3, 3, 10, 10, 22, 22, 22, 30, 30, 30, 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326548 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001465326548 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326548/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326548/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326548 Building ZINC001465326549 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326549' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326549 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465326549 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326549/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326549 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/220 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](Cc3cc(Cl)ccc3OC)C2)cc1Cl) `ZINC001465326549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465326549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001465326549 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](Cc3cc(Cl)ccc3OC)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', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 16, 1, 1, 1, 12, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 2, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 10, 22, 22, 22, 16, 22, 22, 22, 30, 3, 2, 2, 2, 6, 6, 6, 2, 2, 3, 3, 3, 3, 3, 3, 10, 10, 22, 16, 22, 30, 30, 30, 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326549 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326549/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326549 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 221) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/221 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/221' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](Cc3cc(Cl)ccc3OC)C2)cc1Cl) `ZINC001465326549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465326549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001465326549 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](Cc3cc(Cl)ccc3OC)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', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 16, 1, 1, 1, 12, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 2, 5, 5, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 8, 20, 20, 20, 8, 20, 20, 20, 25, 3, 5, 5, 5, 12, 12, 12, 5, 5, 3, 3, 3, 3, 3, 3, 8, 8, 20, 20, 20, 25, 25, 25, 3, 3, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326549 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001465326549 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326549/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326549/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326549 Building ZINC001465326549 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326549' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326549 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465326549 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326549/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326549 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 220) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](Cc3cc(Cl)ccc3OC)C2)cc1Cl) `ZINC001465326549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465326549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001465326549 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](Cc3cc(Cl)ccc3OC)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', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 16, 1, 1, 1, 12, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 2, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 10, 22, 22, 22, 16, 22, 22, 22, 30, 3, 2, 2, 2, 6, 6, 6, 2, 2, 3, 3, 3, 3, 3, 3, 10, 10, 22, 16, 22, 30, 30, 30, 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326549 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326549/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326549 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 221) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](Cc3cc(Cl)ccc3OC)C2)cc1Cl) `ZINC001465326549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465326549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001465326549 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](Cc3cc(Cl)ccc3OC)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', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 16, 1, 1, 1, 12, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 2, 5, 5, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 8, 20, 20, 20, 8, 20, 20, 20, 25, 3, 5, 5, 5, 12, 12, 12, 5, 5, 3, 3, 3, 3, 3, 3, 8, 8, 20, 20, 20, 25, 25, 25, 3, 3, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326549 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001465326549 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326549/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326549/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465326549 Building ZINC001465609461 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465609461' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465609461 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465609461 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465609461/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465609461 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/222 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(Cc2cc(Cl)ccc2Cl)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001465609461.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465609461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465609461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001465609461 none O=C(N1CCC(Cc2cc(Cl)ccc2Cl)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 1, 1, 16, 1, 1, 1, 16, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 5, 5, 5, 5, 15, 26, 26, 26, 26, 26, 26, 26, 5, 5, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 5, 5, 5, 5, 5, 15, 15, 26, 26, 26, 5, 5, 5, 5, 6, 7, 7, 6, 7, 7, 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: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465609461 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465609461/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465609461 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 223) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/223 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/223' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(Cc2cc(Cl)ccc2Cl)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001465609461.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465609461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465609461/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001465609461 none O=C(N1CCC(Cc2cc(Cl)ccc2Cl)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 1, 1, 16, 1, 1, 1, 16, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 5, 5, 5, 5, 13, 26, 26, 26, 24, 26, 26, 26, 5, 5, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 5, 5, 5, 5, 5, 13, 13, 26, 24, 26, 5, 5, 5, 5, 6, 9, 9, 6, 9, 9, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 93 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465609461 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001465609461 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465609461/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465609461/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465609461 Building ZINC001465609461 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465609461' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465609461 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465609461 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465609461/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465609461 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 222) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CCC(Cc2cc(Cl)ccc2Cl)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001465609461.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465609461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465609461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001465609461 none O=C(N1CCC(Cc2cc(Cl)ccc2Cl)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 1, 1, 16, 1, 1, 1, 16, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 5, 5, 5, 5, 15, 26, 26, 26, 26, 26, 26, 26, 5, 5, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 5, 5, 5, 5, 5, 15, 15, 26, 26, 26, 5, 5, 5, 5, 6, 7, 7, 6, 7, 7, 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: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465609461 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465609461/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465609461 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 223) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CCC(Cc2cc(Cl)ccc2Cl)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001465609461.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465609461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465609461/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001465609461 none O=C(N1CCC(Cc2cc(Cl)ccc2Cl)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 1, 1, 16, 1, 1, 1, 16, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 5, 5, 5, 5, 13, 26, 26, 26, 24, 26, 26, 26, 5, 5, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 5, 5, 5, 5, 5, 13, 13, 26, 24, 26, 5, 5, 5, 5, 6, 9, 9, 6, 9, 9, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 93 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465609461 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001465609461 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465609461/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465609461/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465609461 Building ZINC001465774072 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465774072' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465774072 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465774072 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465774072/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465774072 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/224 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(Cc1ccccc1Br)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465774072.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465774072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465774072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001465774072 none CC(C)CN(Cc1ccccc1Br)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 17, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 8, 4, 8, 14, 20, 20, 17, 20, 20, 20, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 14, 14, 20, 20, 20, 20, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 103 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465774072 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465774072/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465774072 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 225) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/225 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/225' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(Cc1ccccc1Br)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465774072.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465774072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465774072/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001465774072 none CC(C)CN(Cc1ccccc1Br)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 17, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 5, 3, 5, 16, 23, 23, 19, 23, 23, 23, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 16, 16, 23, 23, 20, 23, 5, 5, 5, 5] 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]) total number of confs: 111 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465774072 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001465774072 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465774072/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465774072/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465774072 Building ZINC001465774072 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465774072' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465774072 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465774072 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465774072/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465774072 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 224) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)CN(Cc1ccccc1Br)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465774072.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465774072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465774072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001465774072 none CC(C)CN(Cc1ccccc1Br)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 17, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 8, 4, 8, 14, 20, 20, 17, 20, 20, 20, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 14, 14, 20, 20, 20, 20, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 103 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465774072 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465774072/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465774072 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 225) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)CN(Cc1ccccc1Br)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465774072.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465774072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465774072/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001465774072 none CC(C)CN(Cc1ccccc1Br)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 17, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 5, 3, 5, 16, 23, 23, 19, 23, 23, 23, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 16, 16, 23, 23, 20, 23, 5, 5, 5, 5] 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]) total number of confs: 111 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465774072 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001465774072 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465774072/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465774072/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465774072 Building ZINC001465963503 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465963503' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465963503 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465963503 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465963503/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465963503 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/226 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)ccc1NCc1ccccc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001465963503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465963503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465963503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001465963503 none O=C(Nc1cc(Cl)ccc1NCc1ccccc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 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.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, 1, 1, 1, 16, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 4, 7, 7, 7, 17, 24, 31, 31, 28, 31, 31, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 7, 7, 7, 17, 24, 24, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465963503 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465963503/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465963503 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 227) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/227 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/227' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Cl)ccc1NCc1ccccc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001465963503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465963503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465963503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001465963503 none O=C(Nc1cc(Cl)ccc1NCc1ccccc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 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.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, 1, 1, 1, 16, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 2, 7, 7, 7, 17, 26, 32, 32, 28, 32, 32, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 7, 7, 7, 17, 26, 26, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465963503 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001465963503 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465963503/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465963503/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465963503 Building ZINC001465963503 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465963503' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465963503 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465963503 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465963503/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465963503 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 226) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1cc(Cl)ccc1NCc1ccccc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001465963503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465963503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465963503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001465963503 none O=C(Nc1cc(Cl)ccc1NCc1ccccc1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 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.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, 1, 1, 1, 16, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 4, 7, 7, 7, 17, 24, 31, 31, 28, 31, 31, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 7, 7, 7, 17, 24, 24, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465963503 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465963503/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465963503 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 227) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1cc(Cl)ccc1NCc1ccccc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001465963503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465963503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465963503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001465963503 none O=C(Nc1cc(Cl)ccc1NCc1ccccc1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 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.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, 1, 1, 1, 16, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 2, 7, 7, 7, 17, 26, 32, 32, 28, 32, 32, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 7, 7, 7, 17, 26, 26, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465963503 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001465963503 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465963503/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465963503/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001465963503 Building ZINC001466072811 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466072811' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466072811 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466072811 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466072811/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466072811 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/228 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N(CCNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)C1CCCCCC1) `ZINC001466072811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466072811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466072811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001466072811 none CC(C)(C)OC(=O)N(CCNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)C1CCCCCC1 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.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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 13, 19, 11, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 22, 22, 22, 22, 22, 22, 24, 24, 24, 24, 24, 24, 24, 24, 24, 11, 11, 11, 11, 3, 4, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 105 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466072811 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466072811/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466072811 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 229) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/229 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/229' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N(CCNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)C1CCCCCC1) `ZINC001466072811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466072811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466072811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001466072811 none CC(C)(C)OC(=O)N(CCNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)C1CCCCCC1 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.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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 14, 20, 12, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 25, 25, 25, 25, 25, 25, 22, 22, 22, 22, 22, 22, 22, 22, 22, 12, 12, 11, 11, 3, 4, 4, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466072811 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001466072811 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466072811/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466072811/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466072811 Building ZINC001466072811 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466072811' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466072811 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466072811 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466072811/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466072811 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 228) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)OC(=O)N(CCNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)C1CCCCCC1) `ZINC001466072811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466072811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466072811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001466072811 none CC(C)(C)OC(=O)N(CCNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)C1CCCCCC1 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.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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 13, 19, 11, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 22, 22, 22, 22, 22, 22, 24, 24, 24, 24, 24, 24, 24, 24, 24, 11, 11, 11, 11, 3, 4, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 105 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466072811 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466072811/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466072811 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 229) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)OC(=O)N(CCNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)C1CCCCCC1) `ZINC001466072811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466072811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466072811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001466072811 none CC(C)(C)OC(=O)N(CCNC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)C1CCCCCC1 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.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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 14, 20, 12, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 25, 25, 25, 25, 25, 25, 22, 22, 22, 22, 22, 22, 22, 22, 22, 12, 12, 11, 11, 3, 4, 4, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466072811 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001466072811 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466072811/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466072811/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466072811 Building ZINC001466270616 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270616' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270616 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466270616 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270616/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270616 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/230 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN([C@@H](c3ccccc3)c3ccc(Cl)cc3)CC2)c1) `ZINC001466270616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466270616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001466270616 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN([C@@H](c3ccccc3)c3ccc(Cl)cc3)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 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] 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, 7, 7, 7] 0 hydrogens 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, 3, 5, 11, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 22, 22, 22, 22, 22, 22, 11, 11, 6, 6, 6, 6, 2, 6, 6, 11, 11, 11, 11, 20, 20, 20, 20, 20, 22, 22, 22, 22, 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]) total number of confs: 82 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270616 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270616/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270616 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 231) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/231 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/231' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN([C@@H](c3ccccc3)c3ccc(Cl)cc3)CC2)c1) `ZINC001466270616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466270616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001466270616 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN([C@@H](c3ccccc3)c3ccc(Cl)cc3)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 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] 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, 7, 7, 7] 0 hydrogens 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, 3, 6, 14, 14, 14, 14, 22, 22, 24, 24, 22, 24, 24, 22, 24, 24, 22, 24, 24, 24, 14, 14, 6, 6, 6, 6, 2, 6, 6, 14, 14, 14, 14, 24, 24, 24, 24, 24, 24, 24, 24, 24, 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, 54, 55]) total number of confs: 100 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270616 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001466270616 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270616/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270616/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270616 Building ZINC001466270616 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270616' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270616 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466270616 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270616/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270616 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 230) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN([C@@H](c3ccccc3)c3ccc(Cl)cc3)CC2)c1) `ZINC001466270616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466270616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001466270616 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN([C@@H](c3ccccc3)c3ccc(Cl)cc3)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 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] 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, 7, 7, 7] 0 hydrogens 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, 3, 5, 11, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 22, 22, 22, 22, 22, 22, 11, 11, 6, 6, 6, 6, 2, 6, 6, 11, 11, 11, 11, 20, 20, 20, 20, 20, 22, 22, 22, 22, 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]) total number of confs: 82 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270616 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270616/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270616 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 231) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN([C@@H](c3ccccc3)c3ccc(Cl)cc3)CC2)c1) `ZINC001466270616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466270616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001466270616 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN([C@@H](c3ccccc3)c3ccc(Cl)cc3)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 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] 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, 7, 7, 7] 0 hydrogens 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, 3, 6, 14, 14, 14, 14, 22, 22, 24, 24, 22, 24, 24, 22, 24, 24, 22, 24, 24, 24, 14, 14, 6, 6, 6, 6, 2, 6, 6, 14, 14, 14, 14, 24, 24, 24, 24, 24, 24, 24, 24, 24, 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, 54, 55]) total number of confs: 100 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270616 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001466270616 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270616/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270616/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270616 Building ZINC001466270617 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270617' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270617 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466270617 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270617/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270617 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/232 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN([C@H](c3ccccc3)c3ccc(Cl)cc3)CC2)c1) `ZINC001466270617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466270617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001466270617 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN([C@H](c3ccccc3)c3ccc(Cl)cc3)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 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] 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, 7, 7, 7] 0 hydrogens 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, 3, 5, 11, 11, 11, 11, 20, 20, 22, 22, 22, 22, 22, 20, 20, 20, 20, 20, 20, 20, 11, 11, 6, 6, 6, 6, 2, 6, 6, 11, 11, 11, 11, 22, 22, 22, 22, 22, 20, 20, 20, 20, 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]) total number of confs: 82 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270617 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270617/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270617 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 233) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/233 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/233' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN([C@H](c3ccccc3)c3ccc(Cl)cc3)CC2)c1) `ZINC001466270617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466270617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001466270617 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN([C@H](c3ccccc3)c3ccc(Cl)cc3)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 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] 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, 7, 7, 7] 0 hydrogens 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, 3, 6, 15, 15, 15, 15, 26, 26, 28, 28, 28, 28, 28, 26, 28, 28, 26, 26, 28, 28, 15, 15, 6, 6, 6, 6, 2, 6, 6, 15, 15, 15, 15, 28, 28, 28, 28, 28, 28, 28, 28, 28, 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, 54, 55]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270617 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001466270617 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270617/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270617/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270617 Building ZINC001466270617 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270617' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270617 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466270617 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270617/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270617 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 232) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN([C@H](c3ccccc3)c3ccc(Cl)cc3)CC2)c1) `ZINC001466270617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466270617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001466270617 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN([C@H](c3ccccc3)c3ccc(Cl)cc3)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 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] 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, 7, 7, 7] 0 hydrogens 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, 3, 5, 11, 11, 11, 11, 20, 20, 22, 22, 22, 22, 22, 20, 20, 20, 20, 20, 20, 20, 11, 11, 6, 6, 6, 6, 2, 6, 6, 11, 11, 11, 11, 22, 22, 22, 22, 22, 20, 20, 20, 20, 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]) total number of confs: 82 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270617 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270617/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270617 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 233) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN([C@H](c3ccccc3)c3ccc(Cl)cc3)CC2)c1) `ZINC001466270617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466270617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001466270617 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN([C@H](c3ccccc3)c3ccc(Cl)cc3)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 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] 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, 7, 7, 7] 0 hydrogens 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, 3, 6, 15, 15, 15, 15, 26, 26, 28, 28, 28, 28, 28, 26, 28, 28, 26, 26, 28, 28, 15, 15, 6, 6, 6, 6, 2, 6, 6, 15, 15, 15, 15, 28, 28, 28, 28, 28, 28, 28, 28, 28, 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, 54, 55]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270617 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001466270617 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270617/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270617/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466270617 Building ZINC001466281634 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466281634' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466281634 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466281634 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466281634/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466281634 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/234 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc2c(cc(OC(F)(F)F)cc2Br)s1) `ZINC001466281634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466281634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466281634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001466281634 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc2c(cc(OC(F)(F)F)cc2Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need 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, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 18, 19, 19, 19, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 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]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466281634 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466281634/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466281634 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 235) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/235 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/235' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc2c(cc(OC(F)(F)F)cc2Br)s1) `ZINC001466281634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466281634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466281634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001466281634 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc2c(cc(OC(F)(F)F)cc2Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need 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, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 18, 19, 19, 19, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 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]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466281634 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001466281634 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466281634/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466281634/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466281634 Building ZINC001466281634 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466281634' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466281634 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466281634 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466281634/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466281634 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 234) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc2c(cc(OC(F)(F)F)cc2Br)s1) `ZINC001466281634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466281634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466281634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001466281634 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1nc2c(cc(OC(F)(F)F)cc2Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need 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, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 18, 19, 19, 19, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 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]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466281634 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466281634/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466281634 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 235) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc2c(cc(OC(F)(F)F)cc2Br)s1) `ZINC001466281634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466281634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466281634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001466281634 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1nc2c(cc(OC(F)(F)F)cc2Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 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] 0 hydrogens need 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, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 18, 19, 19, 19, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 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]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466281634 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001466281634 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466281634/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466281634/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466281634 Building ZINC001466396218 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001466396218 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/236 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc([N@]2CC[N@](CCc3ccccc3)CC2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001466396218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466396218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001466396218 none O=C(Nc1cccc([N@]2CC[N@](CCc3ccccc3)CC2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 9, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 47, 45, 7, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 7, 2, 2, 2, 2] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 237) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/237 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/237' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc([N@]2CC[N@@](CCc3ccccc3)CC2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001466396218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466396218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001466396218 none O=C(Nc1cccc([N@]2CC[N@@](CCc3ccccc3)CC2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 10, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 47, 45, 8, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 8, 8, 8, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 8, 2, 2, 2, 2] 50 rigid atoms, others: [1, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 238) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/238 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/238' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc([N@]2CC[N@](CCc3ccccc3)CC2)c1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001466396218.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001466396218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001466396218 none O=C(Nc1cccc([N@]2CC[N@](CCc3ccccc3)CC2)c1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 10, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 47, 46, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 7, 7, 7, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 7, 2, 2, 2, 2] 50 rigid atoms, others: [1, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 239) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/239 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/239' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc([N@]2CC[N@@](CCc3ccccc3)CC2)c1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001466396218.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001466396218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001466396218 none O=C(Nc1cccc([N@]2CC[N@@](CCc3ccccc3)CC2)c1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 10, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 47, 46, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 7, 7, 7, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 7, 2, 2, 2, 2] 50 rigid atoms, others: [1, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001466396218 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 Building ZINC001466396218 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001466396218 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 236) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1cccc([N@]2CC[N@](CCc3ccccc3)CC2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001466396218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466396218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001466396218 none O=C(Nc1cccc([N@]2CC[N@](CCc3ccccc3)CC2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 9, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 47, 45, 7, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 7, 2, 2, 2, 2] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 237) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1cccc([N@]2CC[N@@](CCc3ccccc3)CC2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001466396218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466396218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001466396218 none O=C(Nc1cccc([N@]2CC[N@@](CCc3ccccc3)CC2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 10, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 47, 45, 8, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 8, 8, 8, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 8, 2, 2, 2, 2] 50 rigid atoms, others: [1, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 238) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/238: 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(Nc1cccc([N@]2CC[N@](CCc3ccccc3)CC2)c1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001466396218.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001466396218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001466396218 none O=C(Nc1cccc([N@]2CC[N@](CCc3ccccc3)CC2)c1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 10, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 47, 46, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 7, 7, 7, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 7, 2, 2, 2, 2] 50 rigid atoms, others: [1, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 239) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/239: 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(Nc1cccc([N@]2CC[N@@](CCc3ccccc3)CC2)c1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001466396218.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001466396218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001466396218 none O=C(Nc1cccc([N@]2CC[N@@](CCc3ccccc3)CC2)c1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 10, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 47, 46, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 7, 7, 7, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 7, 2, 2, 2, 2] 50 rigid atoms, others: [1, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001466396218 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 Building ZINC001466396218 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001466396218 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 236) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1cccc([N@]2CC[N@](CCc3ccccc3)CC2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001466396218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466396218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001466396218 none O=C(Nc1cccc([N@]2CC[N@](CCc3ccccc3)CC2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 9, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 47, 45, 7, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 7, 2, 2, 2, 2] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 237) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1cccc([N@]2CC[N@@](CCc3ccccc3)CC2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001466396218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466396218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001466396218 none O=C(Nc1cccc([N@]2CC[N@@](CCc3ccccc3)CC2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 10, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 47, 45, 8, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 8, 8, 8, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 8, 2, 2, 2, 2] 50 rigid atoms, others: [1, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 238) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/238: 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(Nc1cccc([N@]2CC[N@](CCc3ccccc3)CC2)c1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001466396218.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001466396218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001466396218 none O=C(Nc1cccc([N@]2CC[N@](CCc3ccccc3)CC2)c1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 10, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 47, 46, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 7, 7, 7, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 7, 2, 2, 2, 2] 50 rigid atoms, others: [1, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 239) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/239: 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(Nc1cccc([N@]2CC[N@@](CCc3ccccc3)CC2)c1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001466396218.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001466396218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001466396218 none O=C(Nc1cccc([N@]2CC[N@@](CCc3ccccc3)CC2)c1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 10, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 47, 46, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 7, 7, 7, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 7, 2, 2, 2, 2] 50 rigid atoms, others: [1, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001466396218 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 Building ZINC001466396218 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001466396218 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 236) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1cccc([N@]2CC[N@](CCc3ccccc3)CC2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001466396218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466396218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001466396218 none O=C(Nc1cccc([N@]2CC[N@](CCc3ccccc3)CC2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 9, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 47, 45, 7, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 7, 2, 2, 2, 2] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 237) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1cccc([N@]2CC[N@@](CCc3ccccc3)CC2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001466396218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466396218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001466396218 none O=C(Nc1cccc([N@]2CC[N@@](CCc3ccccc3)CC2)c1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 10, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 47, 45, 8, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 8, 8, 8, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 8, 2, 2, 2, 2] 50 rigid atoms, others: [1, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 238) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/238: 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(Nc1cccc([N@]2CC[N@](CCc3ccccc3)CC2)c1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001466396218.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001466396218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001466396218 none O=C(Nc1cccc([N@]2CC[N@](CCc3ccccc3)CC2)c1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 10, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 47, 46, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 7, 7, 7, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 7, 2, 2, 2, 2] 50 rigid atoms, others: [1, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 239) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/239: 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(Nc1cccc([N@]2CC[N@@](CCc3ccccc3)CC2)c1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001466396218.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001466396218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001466396218 none O=C(Nc1cccc([N@]2CC[N@@](CCc3ccccc3)CC2)c1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 5, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 7, 7, 10, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 47, 46, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 7, 7, 7, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 7, 2, 2, 2, 2] 50 rigid atoms, others: [1, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001466396218 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466396218 Building ZINC001466579237 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466579237' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466579237 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466579237 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466579237/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466579237 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/240 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Nc2ccc(F)cc2F)c(Br)c1) `ZINC001466579237.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466579237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466579237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001466579237 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Nc2ccc(F)cc2F)c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 15, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need 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, 1, 1, 1, 1, 3, 3, 3, 12, 12, 9, 12, 41, 44, 44, 43, 44, 44, 44, 44, 12, 12, 12, 4, 4, 4, 4, 4, 4, 3, 12, 12, 41, 44, 44, 44, 12] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 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: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466579237 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466579237/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466579237 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 241) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/241 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/241' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Nc2ccc(F)cc2F)c(Br)c1) `ZINC001466579237.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466579237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466579237/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001466579237 none Cn1cccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Nc2ccc(F)cc2F)c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 15, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 11, 11, 8, 11, 41, 44, 44, 43, 43, 44, 44, 44, 11, 11, 11, 4, 4, 4, 4, 4, 4, 2, 11, 11, 41, 44, 44, 44, 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, 37, 38, 39, 40]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466579237 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001466579237 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466579237/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466579237/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466579237 Building ZINC001466579237 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466579237' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466579237 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466579237 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466579237/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466579237 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 240) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Nc2ccc(F)cc2F)c(Br)c1) `ZINC001466579237.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466579237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466579237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001466579237 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Nc2ccc(F)cc2F)c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 15, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need 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, 1, 1, 1, 1, 3, 3, 3, 12, 12, 9, 12, 41, 44, 44, 43, 44, 44, 44, 44, 12, 12, 12, 4, 4, 4, 4, 4, 4, 3, 12, 12, 41, 44, 44, 44, 12] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 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: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466579237 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466579237/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466579237 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 241) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Nc2ccc(F)cc2F)c(Br)c1) `ZINC001466579237.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466579237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466579237/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001466579237 none Cn1cccc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Nc2ccc(F)cc2F)c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 15, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need 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, 1, 1, 1, 1, 2, 2, 2, 11, 11, 8, 11, 41, 44, 44, 43, 43, 44, 44, 44, 11, 11, 11, 4, 4, 4, 4, 4, 4, 2, 11, 11, 41, 44, 44, 44, 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, 37, 38, 39, 40]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466579237 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001466579237 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466579237/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466579237/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466579237 Building ZINC001466845287 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466845287' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466845287 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466845287 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466845287/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466845287 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/242 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/242' -> `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)Nc1cnn(c2ccc(C)cc2)c1C(C)C) `ZINC001466845287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466845287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466845287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001466845287 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnn(c2ccc(C)cc2)c1C(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.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 12, 12, 4, 4, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 31, 31, 17, 20, 31, 31, 17, 17, 17, 17, 4, 4, 4, 12, 12, 6, 12, 12, 4, 4, 4, 6, 17, 31, 31, 31, 31, 31, 31, 31, 17, 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: 191 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466845287 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466845287/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466845287 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 243) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/243 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/243' -> `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)Nc1cnn(c2ccc(C)cc2)c1C(C)C) `ZINC001466845287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466845287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466845287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001466845287 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnn(c2ccc(C)cc2)c1C(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.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 18, 18, 18, 18, 30, 30, 29, 30, 30, 30, 18, 18, 18, 18, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 4, 6, 18, 30, 30, 30, 30, 30, 30, 30, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 90 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466845287 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001466845287 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466845287/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466845287/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466845287 Building ZINC001466845287 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466845287' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466845287 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466845287 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466845287/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466845287 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 242) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/242: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnn(c2ccc(C)cc2)c1C(C)C) `ZINC001466845287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466845287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466845287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001466845287 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnn(c2ccc(C)cc2)c1C(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.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 12, 12, 4, 4, 1, 1, 1, 1, 6, 6, 6, 17, 17, 17, 17, 31, 31, 17, 20, 31, 31, 17, 17, 17, 17, 4, 4, 4, 12, 12, 6, 12, 12, 4, 4, 4, 6, 17, 31, 31, 31, 31, 31, 31, 31, 17, 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: 191 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466845287 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466845287/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466845287 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 243) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/243: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnn(c2ccc(C)cc2)c1C(C)C) `ZINC001466845287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466845287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466845287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001466845287 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnn(c2ccc(C)cc2)c1C(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.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 18, 18, 18, 18, 30, 30, 29, 30, 30, 30, 18, 18, 18, 18, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 4, 6, 18, 30, 30, 30, 30, 30, 30, 30, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 90 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466845287 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001466845287 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466845287/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466845287/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001466845287 Building ZINC001467267801 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267801' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267801 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467267801 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267801/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267801 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/244 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)c1ccccc1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001467267801.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467267801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001467267801 none CC(C)(C)OC(=O)c1ccccc1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 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', 'C.ar', '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', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 32, 13, 32, 13, 13, 6, 13, 13, 6, 6, 6, 6, 4, 2, 5, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 13, 13, 13, 13, 6, 6, 6, 6, 6, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 123 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267801 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267801/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267801 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 245) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/245 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/245' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)c1ccccc1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001467267801.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467267801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001467267801 none CC(C)(C)OC(=O)c1ccccc1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 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', 'C.ar', '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', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 31, 12, 31, 12, 12, 6, 12, 12, 6, 6, 6, 6, 4, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 36, 36, 36, 36, 36, 36, 36, 36, 36, 12, 12, 12, 12, 6, 6, 6, 6, 6, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267801 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001467267801 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267801/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267801/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267801 Building ZINC001467267801 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267801' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267801 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467267801 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267801/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267801 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 244) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)OC(=O)c1ccccc1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001467267801.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467267801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001467267801 none CC(C)(C)OC(=O)c1ccccc1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 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', 'C.ar', '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', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 32, 13, 32, 13, 13, 6, 13, 13, 6, 6, 6, 6, 4, 2, 5, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 13, 13, 13, 13, 6, 6, 6, 6, 6, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 123 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267801 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267801/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267801 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 245) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)OC(=O)c1ccccc1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001467267801.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467267801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001467267801 none CC(C)(C)OC(=O)c1ccccc1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 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', 'C.ar', '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', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 31, 12, 31, 12, 12, 6, 12, 12, 6, 6, 6, 6, 4, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 36, 36, 36, 36, 36, 36, 36, 36, 36, 12, 12, 12, 12, 6, 6, 6, 6, 6, 2, 2, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267801 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001467267801 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267801/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267801/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267801 Building ZINC001467267856 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267856' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267856 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467267856 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267856/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267856 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/246 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)c1ccccc1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001467267856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467267856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001467267856 none CC(C)(C)OC(=O)c1ccccc1C1CCN(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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 20, 44, 20, 20, 20, 20, 20, 11, 11, 11, 11, 6, 2, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 11, 11, 11, 11, 11, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [51, 48, 49, 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, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 52, 53, 54, 55]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267856 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267856/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267856 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 247) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/247 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/247' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)c1ccccc1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001467267856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467267856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001467267856 none CC(C)(C)OC(=O)c1ccccc1C1CCN(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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 18, 44, 18, 18, 18, 18, 18, 11, 11, 11, 11, 6, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 11, 11, 11, 11, 11, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [51, 49, 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, 47, 52, 53, 54, 55]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267856 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001467267856 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267856/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267856/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267856 Building ZINC001467267856 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267856' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267856 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467267856 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267856/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267856 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 246) grep: /scratch/xiaobo/12845/xbi-8058088.35/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)(C)OC(=O)c1ccccc1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001467267856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467267856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001467267856 none CC(C)(C)OC(=O)c1ccccc1C1CCN(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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 20, 44, 20, 20, 20, 20, 20, 11, 11, 11, 11, 6, 2, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 20, 11, 11, 11, 11, 11, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [51, 48, 49, 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, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 52, 53, 54, 55]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267856 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267856/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267856 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 247) grep: /scratch/xiaobo/12845/xbi-8058088.35/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)(C)OC(=O)c1ccccc1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001467267856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467267856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001467267856 none CC(C)(C)OC(=O)c1ccccc1C1CCN(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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 18, 44, 18, 18, 18, 18, 18, 11, 11, 11, 11, 6, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 11, 11, 11, 11, 11, 1, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [51, 49, 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, 47, 52, 53, 54, 55]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267856 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001467267856 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267856/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267856/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467267856 Building ZINC001467284711 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284711' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284711 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467284711 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284711/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284711 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/248 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc2ccccc2n1[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001467284711.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467284711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001467284711 none CCc1nc2ccccc2n1[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 34, 34, 34, 34, 34, 34, 34, 15, 15, 15, 15, 15, 15, 9, 2, 7, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 46, 46, 46, 46, 46, 34, 34, 34, 34, 15, 15, 15, 15, 15, 15, 3, 1, 3, 15, 15] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 132 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284711 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284711/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284711 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 249) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/249 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/249' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc2ccccc2n1[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001467284711.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467284711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284711/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001467284711 none CCc1nc2ccccc2n1[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 33, 33, 33, 33, 33, 33, 33, 14, 14, 14, 14, 14, 14, 7, 2, 5, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 14, 46, 46, 46, 46, 46, 33, 33, 33, 33, 14, 14, 14, 14, 14, 14, 4, 1, 4, 14, 14] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 134 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284711 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001467284711 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284711/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284711/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284711 Building ZINC001467284711 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284711' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284711 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467284711 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284711/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284711 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 248) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCc1nc2ccccc2n1[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001467284711.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467284711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001467284711 none CCc1nc2ccccc2n1[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 34, 34, 34, 34, 34, 34, 34, 15, 15, 15, 15, 15, 15, 9, 2, 7, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 46, 46, 46, 46, 46, 34, 34, 34, 34, 15, 15, 15, 15, 15, 15, 3, 1, 3, 15, 15] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 132 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284711 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284711/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284711 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 249) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCc1nc2ccccc2n1[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001467284711.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467284711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284711/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001467284711 none CCc1nc2ccccc2n1[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 33, 33, 33, 33, 33, 33, 33, 14, 14, 14, 14, 14, 14, 7, 2, 5, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 14, 46, 46, 46, 46, 46, 33, 33, 33, 33, 14, 14, 14, 14, 14, 14, 4, 1, 4, 14, 14] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 134 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284711 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001467284711 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284711/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284711/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284711 Building ZINC001467284714 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284714' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284714 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467284714 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284714/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284714 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/250 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc2ccccc2n1[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001467284714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467284714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001467284714 none CCc1nc2ccccc2n1[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 34, 34, 34, 34, 34, 34, 34, 15, 15, 15, 15, 15, 15, 8, 2, 6, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 15, 47, 47, 47, 47, 47, 34, 34, 34, 34, 15, 15, 15, 15, 15, 15, 4, 1, 4, 15, 15] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 132 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284714 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284714/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284714 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 251) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/251 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/251' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc2ccccc2n1[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001467284714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467284714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001467284714 none CCc1nc2ccccc2n1[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 34, 34, 34, 34, 34, 34, 34, 14, 14, 14, 14, 14, 14, 8, 2, 6, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 14, 47, 47, 47, 47, 47, 34, 34, 34, 34, 14, 14, 14, 14, 14, 14, 4, 1, 4, 14, 14] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 138 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284714 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001467284714 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284714/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284714/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284714 Building ZINC001467284714 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284714' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284714 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467284714 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284714/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284714 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 250) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCc1nc2ccccc2n1[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001467284714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467284714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001467284714 none CCc1nc2ccccc2n1[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 34, 34, 34, 34, 34, 34, 34, 15, 15, 15, 15, 15, 15, 8, 2, 6, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 15, 47, 47, 47, 47, 47, 34, 34, 34, 34, 15, 15, 15, 15, 15, 15, 4, 1, 4, 15, 15] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 132 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284714 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284714/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284714 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 251) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCc1nc2ccccc2n1[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001467284714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467284714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001467284714 none CCc1nc2ccccc2n1[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 34, 34, 34, 34, 34, 34, 34, 14, 14, 14, 14, 14, 14, 8, 2, 6, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 14, 47, 47, 47, 47, 47, 34, 34, 34, 34, 14, 14, 14, 14, 14, 14, 4, 1, 4, 14, 14] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 138 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284714 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001467284714 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284714/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284714/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467284714 Building ZINC001467375264 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375264' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375264 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467375264 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375264/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375264 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/252 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](c2cc(C(F)(F)F)cc(C(F)(F)F)c2)C1) `ZINC001467375264.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467375264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001467375264 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](c2cc(C(F)(F)F)cc(C(F)(F)F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 4, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 4, 17, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 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]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375264 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375264/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375264 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 253) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/253 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/253' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCO[C@H](c2cc(C(F)(F)F)cc(C(F)(F)F)c2)C1) `ZINC001467375264.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467375264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375264/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001467375264 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCO[C@H](c2cc(C(F)(F)F)cc(C(F)(F)F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 7, 18, 18, 18, 18, 18, 18, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 18, 7, 18, 4, 4] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375264 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001467375264 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375264/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375264/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375264 Building ZINC001467375264 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375264' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375264 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467375264 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375264/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375264 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 252) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](c2cc(C(F)(F)F)cc(C(F)(F)F)c2)C1) `ZINC001467375264.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467375264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001467375264 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](c2cc(C(F)(F)F)cc(C(F)(F)F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 4, 17, 17, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 4, 17, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 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]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375264 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375264/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375264 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 253) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCO[C@H](c2cc(C(F)(F)F)cc(C(F)(F)F)c2)C1) `ZINC001467375264.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467375264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375264/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001467375264 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCO[C@H](c2cc(C(F)(F)F)cc(C(F)(F)F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 7, 18, 18, 18, 18, 18, 18, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 18, 7, 18, 4, 4] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375264 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001467375264 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375264/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375264/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375264 Building ZINC001467375267 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375267' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375267 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467375267 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375267/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375267 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/254 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](c2cc(C(F)(F)F)cc(C(F)(F)F)c2)C1) `ZINC001467375267.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467375267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001467375267 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](c2cc(C(F)(F)F)cc(C(F)(F)F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 18, 3, 3] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375267 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375267/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375267 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 255) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/255 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/255' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](c2cc(C(F)(F)F)cc(C(F)(F)F)c2)C1) `ZINC001467375267.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467375267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375267/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001467375267 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](c2cc(C(F)(F)F)cc(C(F)(F)F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18, 18, 18, 3, 18, 18, 18, 18, 18, 18, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 18, 3, 18, 2, 2] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375267 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001467375267 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375267/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375267/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375267 Building ZINC001467375267 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375267' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375267 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467375267 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375267/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375267 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 254) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](c2cc(C(F)(F)F)cc(C(F)(F)F)c2)C1) `ZINC001467375267.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467375267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001467375267 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](c2cc(C(F)(F)F)cc(C(F)(F)F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 18, 3, 3] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375267 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375267/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375267 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 255) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](c2cc(C(F)(F)F)cc(C(F)(F)F)c2)C1) `ZINC001467375267.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467375267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375267/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001467375267 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](c2cc(C(F)(F)F)cc(C(F)(F)F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 15, 15, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18, 18, 18, 3, 18, 18, 18, 18, 18, 18, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 18, 3, 18, 2, 2] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375267 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001467375267 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375267/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375267/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467375267 Building ZINC001467482240 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467482240' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467482240 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467482240 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467482240/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467482240 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/256 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Oc2ccc(F)cc2)c(Br)c1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001467482240.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467482240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467482240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001467482240 none O=C(Nc1ccc(Oc2ccc(F)cc2)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', 'F', 'C.ar', '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, 15, 1, 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: [3, 1, 3, 3, 13, 13, 10, 10, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 13, 13, 50, 50, 50, 50, 13, 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: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467482240 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467482240/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467482240 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 257) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/257 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/257' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Oc2ccc(F)cc2)c(Br)c1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001467482240.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467482240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467482240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001467482240 none O=C(Nc1ccc(Oc2ccc(F)cc2)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', 'F', 'C.ar', '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, 15, 1, 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: [3, 1, 3, 3, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 13, 13, 50, 50, 50, 50, 13, 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: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467482240 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001467482240 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467482240/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467482240/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467482240 Building ZINC001467482240 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467482240' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467482240 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467482240 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467482240/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467482240 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 256) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ccc(Oc2ccc(F)cc2)c(Br)c1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001467482240.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467482240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467482240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001467482240 none O=C(Nc1ccc(Oc2ccc(F)cc2)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', 'F', 'C.ar', '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, 15, 1, 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: [3, 1, 3, 3, 13, 13, 10, 10, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 13, 13, 50, 50, 50, 50, 13, 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: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467482240 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467482240/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467482240 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 257) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ccc(Oc2ccc(F)cc2)c(Br)c1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001467482240.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467482240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467482240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001467482240 none O=C(Nc1ccc(Oc2ccc(F)cc2)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', 'F', 'C.ar', '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, 15, 1, 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: [3, 1, 3, 3, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 13, 13, 50, 50, 50, 50, 13, 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: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467482240 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001467482240 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467482240/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467482240/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467482240 Building ZINC001467514786 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467514786' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467514786 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467514786 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467514786/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467514786 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/258 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(F)(c2ccccc2C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001467514786.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467514786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467514786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001467514786 none O=C(N1CCC(F)(c2ccccc2C(F)(F)F)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', 'F', '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.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 15, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 33 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467514786 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467514786/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467514786 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 259) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/259 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/259' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(F)(c2ccccc2C(F)(F)F)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001467514786.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467514786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467514786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001467514786 none O=C(N1CCC(F)(c2ccccc2C(F)(F)F)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', 'F', '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.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 15, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 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, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 40 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467514786 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001467514786 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467514786/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467514786/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467514786 Building ZINC001467514786 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467514786' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467514786 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467514786 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467514786/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467514786 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 258) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CCC(F)(c2ccccc2C(F)(F)F)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001467514786.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467514786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467514786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001467514786 none O=C(N1CCC(F)(c2ccccc2C(F)(F)F)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', 'F', '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.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 15, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 33 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467514786 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467514786/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467514786 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 259) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CCC(F)(c2ccccc2C(F)(F)F)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001467514786.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467514786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467514786/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001467514786 none O=C(N1CCC(F)(c2ccccc2C(F)(F)F)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', 'F', '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.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 15, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 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, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 40 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467514786 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001467514786 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467514786/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467514786/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467514786 Building ZINC001467907470 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467907470' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467907470 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467907470 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467907470/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467907470 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/260 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)cc(Oc2cccc(CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)c1) `ZINC001467907470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467907470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467907470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001467907470 none COc1cc(OC)cc(Oc2cccc(CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 29, 29, 30, 29, 26, 18, 18, 18, 18, 18, 9, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 29, 29, 29, 29, 26, 30, 30, 30, 29, 18, 18, 18, 9, 9, 3, 4, 4, 4, 4, 18, 29] 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467907470 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467907470/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467907470 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 261) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/261 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/261' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(OC)cc(Oc2cccc(CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)c1) `ZINC001467907470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467907470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467907470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001467907470 none COc1cc(OC)cc(Oc2cccc(CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 29, 29, 29, 29, 27, 18, 18, 18, 18, 18, 9, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 29, 30, 30, 30, 27, 29, 29, 29, 29, 18, 18, 18, 9, 9, 3, 4, 4, 4, 4, 18, 29] 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467907470 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001467907470 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467907470/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467907470/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467907470 Building ZINC001467907470 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467907470' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467907470 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467907470 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467907470/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467907470 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 260) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1cc(OC)cc(Oc2cccc(CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)c1) `ZINC001467907470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467907470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467907470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001467907470 none COc1cc(OC)cc(Oc2cccc(CNC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 29, 29, 30, 29, 26, 18, 18, 18, 18, 18, 9, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 29, 29, 29, 29, 26, 30, 30, 30, 29, 18, 18, 18, 9, 9, 3, 4, 4, 4, 4, 18, 29] 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467907470 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467907470/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467907470 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 261) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1cc(OC)cc(Oc2cccc(CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)c1) `ZINC001467907470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467907470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467907470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001467907470 none COc1cc(OC)cc(Oc2cccc(CNC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)c2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 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] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 29, 29, 29, 29, 27, 18, 18, 18, 18, 18, 9, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 29, 30, 30, 30, 27, 29, 29, 29, 29, 18, 18, 18, 9, 9, 3, 4, 4, 4, 4, 18, 29] 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467907470 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001467907470 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467907470/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467907470/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467907470 Building ZINC001467972758 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972758' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972758 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467972758 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972758/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972758 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/262 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1cccc(C(F)(F)F)c1)C1CCOCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001467972758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467972758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001467972758 none O=C(N[C@H](c1cccc(C(F)(F)F)c1)C1CCOCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 5, 12, 5, 5, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need 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, 17, 17, 13, 17, 17, 17, 17, 17, 17, 9, 11, 11, 11, 11, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 17, 17, 13, 17, 11, 11, 11, 11, 11, 11, 11, 11, 11, 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972758 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972758/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972758 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 263) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/263 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/263' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](c1cccc(C(F)(F)F)c1)C1CCOCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001467972758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467972758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001467972758 none O=C(N[C@H](c1cccc(C(F)(F)F)c1)C1CCOCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 5, 12, 5, 5, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need 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, 6, 6, 17, 17, 12, 17, 17, 17, 17, 17, 17, 10, 15, 15, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 17, 17, 12, 17, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 7, 7, 7] 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972758 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001467972758 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972758/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972758/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972758 Building ZINC001467972758 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972758' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972758 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467972758 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972758/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972758 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 262) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(N[C@H](c1cccc(C(F)(F)F)c1)C1CCOCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001467972758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467972758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001467972758 none O=C(N[C@H](c1cccc(C(F)(F)F)c1)C1CCOCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 5, 12, 5, 5, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need 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, 17, 17, 13, 17, 17, 17, 17, 17, 17, 9, 11, 11, 11, 11, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 17, 17, 13, 17, 11, 11, 11, 11, 11, 11, 11, 11, 11, 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972758 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972758/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972758 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 263) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(N[C@H](c1cccc(C(F)(F)F)c1)C1CCOCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001467972758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467972758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001467972758 none O=C(N[C@H](c1cccc(C(F)(F)F)c1)C1CCOCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 5, 12, 5, 5, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need 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, 6, 6, 17, 17, 12, 17, 17, 17, 17, 17, 17, 10, 15, 15, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 17, 17, 12, 17, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 7, 7, 7] 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972758 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001467972758 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972758/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972758/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972758 Building ZINC001467972759 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972759' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972759 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467972759 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972759/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972759 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/264 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1cccc(C(F)(F)F)c1)C1CCOCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001467972759.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467972759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001467972759 none O=C(N[C@@H](c1cccc(C(F)(F)F)c1)C1CCOCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 5, 12, 5, 5, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need 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, 6, 6, 16, 16, 12, 16, 16, 16, 16, 16, 16, 10, 15, 15, 15, 15, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 16, 16, 12, 16, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972759 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972759/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972759 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 265) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/265 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/265' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](c1cccc(C(F)(F)F)c1)C1CCOCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001467972759.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467972759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972759/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001467972759 none O=C(N[C@@H](c1cccc(C(F)(F)F)c1)C1CCOCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 5, 12, 5, 5, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need 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, 17, 17, 13, 17, 17, 17, 17, 17, 17, 10, 12, 12, 12, 12, 12, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 17, 17, 13, 17, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972759 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001467972759 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972759/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972759/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972759 Building ZINC001467972759 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972759' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972759 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467972759 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972759/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972759 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 264) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N[C@@H](c1cccc(C(F)(F)F)c1)C1CCOCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001467972759.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467972759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001467972759 none O=C(N[C@@H](c1cccc(C(F)(F)F)c1)C1CCOCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 5, 12, 5, 5, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need 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, 6, 6, 16, 16, 12, 16, 16, 16, 16, 16, 16, 10, 15, 15, 15, 15, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 16, 16, 12, 16, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972759 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972759/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972759 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 265) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N[C@@H](c1cccc(C(F)(F)F)c1)C1CCOCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001467972759.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467972759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972759/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001467972759 none O=C(N[C@@H](c1cccc(C(F)(F)F)c1)C1CCOCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 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.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 5, 12, 5, 5, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need 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, 17, 17, 13, 17, 17, 17, 17, 17, 17, 10, 12, 12, 12, 12, 12, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 17, 17, 13, 17, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972759 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001467972759 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972759/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972759/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467972759 Building ZINC001467980584 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467980584' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467980584 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467980584 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467980584/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467980584 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/266 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(c1ccccc1)S(=O)(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1) `ZINC001467980584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467980584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467980584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001467980584 none CCCCN(c1ccccc1)S(=O)(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 13, 9, 13, 13, 13, 13, 13, 13, 5, 9, 9, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 5, 18, 18, 18, 18, 18, 18, 18, 16, 16, 13, 13, 13, 13, 13, 5, 5, 5, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 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, 56, 57, 58, 59]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467980584 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467980584/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467980584 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 267) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/267 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/267' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(c1ccccc1)S(=O)(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1) `ZINC001467980584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467980584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467980584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001467980584 none CCCCN(c1ccccc1)S(=O)(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 13, 9, 13, 13, 13, 13, 13, 13, 5, 9, 9, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 5, 18, 18, 18, 18, 18, 18, 18, 16, 16, 13, 13, 13, 13, 13, 5, 5, 5, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 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, 56, 57, 58, 59]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467980584 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001467980584 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467980584/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467980584/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467980584 Building ZINC001467980584 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467980584' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467980584 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467980584 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467980584/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467980584 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 266) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCCCN(c1ccccc1)S(=O)(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1) `ZINC001467980584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467980584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467980584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001467980584 none CCCCN(c1ccccc1)S(=O)(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 13, 9, 13, 13, 13, 13, 13, 13, 5, 9, 9, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 5, 18, 18, 18, 18, 18, 18, 18, 16, 16, 13, 13, 13, 13, 13, 5, 5, 5, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 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, 56, 57, 58, 59]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467980584 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467980584/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467980584 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 267) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCCCN(c1ccccc1)S(=O)(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1) `ZINC001467980584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467980584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467980584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001467980584 none CCCCN(c1ccccc1)S(=O)(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 13, 9, 13, 13, 13, 13, 13, 13, 5, 9, 9, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 5, 18, 18, 18, 18, 18, 18, 18, 16, 16, 13, 13, 13, 13, 13, 5, 5, 5, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 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, 56, 57, 58, 59]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467980584 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001467980584 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467980584/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467980584/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001467980584 Building ZINC001468233176 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468233176' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468233176 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468233176 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468233176/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468233176 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/268 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(CN(C)C(=O)OC(C)(C)C)cc2)cc1Cl) `ZINC001468233176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468233176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468233176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001468233176 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(CN(C)C(=O)OC(C)(C)C)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.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 8, 5, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 17, 17, 27, 27, 27, 27, 27, 27, 2, 2, 2, 2, 2, 4, 4, 4, 2, 2, 1, 2, 2, 7, 7, 17, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 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: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468233176 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468233176/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468233176 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 269) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/269 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/269' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(CN(C)C(=O)OC(C)(C)C)cc2)cc1Cl) `ZINC001468233176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468233176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468233176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001468233176 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(CN(C)C(=O)OC(C)(C)C)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.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 8, 5, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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: [5, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 3, 3, 2, 3, 9, 18, 18, 28, 28, 28, 28, 28, 28, 3, 3, 3, 3, 3, 5, 5, 5, 3, 3, 2, 3, 3, 9, 9, 18, 18, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 3, 3, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468233176 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001468233176 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468233176/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468233176/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468233176 Building ZINC001468233176 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468233176' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468233176 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468233176 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468233176/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468233176 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 268) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(CN(C)C(=O)OC(C)(C)C)cc2)cc1Cl) `ZINC001468233176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468233176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468233176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001468233176 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(CN(C)C(=O)OC(C)(C)C)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.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 8, 5, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 7, 17, 17, 27, 27, 27, 27, 27, 27, 2, 2, 2, 2, 2, 4, 4, 4, 2, 2, 1, 2, 2, 7, 7, 17, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 2, 2, 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: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468233176 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468233176/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468233176 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 269) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(CN(C)C(=O)OC(C)(C)C)cc2)cc1Cl) `ZINC001468233176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468233176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468233176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001468233176 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(CN(C)C(=O)OC(C)(C)C)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.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 8, 5, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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: [5, 3, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 3, 3, 2, 3, 9, 18, 18, 28, 28, 28, 28, 28, 28, 3, 3, 3, 3, 3, 5, 5, 5, 3, 3, 2, 3, 3, 9, 9, 18, 18, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 3, 3, 3] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468233176 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001468233176 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468233176/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468233176/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468233176 Building ZINC001468268844 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268844' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268844 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468268844 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268844/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268844 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/270 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2nc3cc(Cl)c(Cl)cc3[nH]2)cc1Cl) `ZINC001468268844.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468268844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001468268844 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2nc3cc(Cl)c(Cl)cc3[nH]2)cc1Cl NO_LONG_NAME dock atom 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 16, 1, 16, 1, 1, 8, 6, 1, 1, 16, 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, 4, 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] 0 hydrogens 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, 3, 3, 3, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 12, 12, 12, 6, 6, 3, 6, 6, 6, 18, 18, 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268844 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268844/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268844 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 271) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/271 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/271' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2nc3cc(Cl)c(Cl)cc3[nH]2)cc1Cl) `ZINC001468268844.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468268844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001468268844 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2nc3cc(Cl)c(Cl)cc3[nH]2)cc1Cl NO_LONG_NAME dock atom 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 16, 1, 16, 1, 1, 8, 6, 1, 1, 16, 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, 4, 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] 0 hydrogens 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, 4, 4, 4, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 13, 13, 13, 6, 6, 4, 6, 6, 6, 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268844 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001468268844 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268844/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268844/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268844 Building ZINC001468268844 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268844' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268844 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468268844 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268844/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268844 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 270) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2nc3cc(Cl)c(Cl)cc3[nH]2)cc1Cl) `ZINC001468268844.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468268844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001468268844 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2nc3cc(Cl)c(Cl)cc3[nH]2)cc1Cl NO_LONG_NAME dock atom 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 16, 1, 16, 1, 1, 8, 6, 1, 1, 16, 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, 4, 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] 0 hydrogens 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, 3, 3, 3, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 12, 12, 12, 6, 6, 3, 6, 6, 6, 18, 18, 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268844 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268844/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268844 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 271) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2nc3cc(Cl)c(Cl)cc3[nH]2)cc1Cl) `ZINC001468268844.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468268844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001468268844 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2nc3cc(Cl)c(Cl)cc3[nH]2)cc1Cl NO_LONG_NAME dock atom 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 16, 1, 16, 1, 1, 8, 6, 1, 1, 16, 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, 4, 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] 0 hydrogens 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, 4, 4, 4, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 13, 13, 13, 6, 6, 4, 6, 6, 6, 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268844 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001468268844 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268844/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268844/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268844 Building ZINC001468268845 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268845' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268845 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468268845 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268845/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268845 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/272 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2nc3cc(Cl)c(Cl)cc3[nH]2)cc1Cl) `ZINC001468268845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468268845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001468268845 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2nc3cc(Cl)c(Cl)cc3[nH]2)cc1Cl NO_LONG_NAME dock atom 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 16, 1, 16, 1, 1, 8, 6, 1, 1, 16, 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, 4, 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] 0 hydrogens 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, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 12, 12, 12, 6, 6, 4, 6, 6, 6, 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268845 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268845/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268845 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 273) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/273 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/273' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2nc3cc(Cl)c(Cl)cc3[nH]2)cc1Cl) `ZINC001468268845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468268845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001468268845 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2nc3cc(Cl)c(Cl)cc3[nH]2)cc1Cl NO_LONG_NAME dock atom 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 16, 1, 16, 1, 1, 8, 6, 1, 1, 16, 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, 4, 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] 0 hydrogens 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, 3, 3, 3, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 12, 12, 12, 6, 6, 3, 6, 6, 6, 18, 18, 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268845 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001468268845 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268845/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268845/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268845 Building ZINC001468268845 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268845' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268845 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468268845 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268845/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268845 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 272) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2nc3cc(Cl)c(Cl)cc3[nH]2)cc1Cl) `ZINC001468268845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468268845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001468268845 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2nc3cc(Cl)c(Cl)cc3[nH]2)cc1Cl NO_LONG_NAME dock atom 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 16, 1, 16, 1, 1, 8, 6, 1, 1, 16, 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, 4, 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] 0 hydrogens 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, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 12, 12, 12, 6, 6, 4, 6, 6, 6, 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268845 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268845/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268845 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 273) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2nc3cc(Cl)c(Cl)cc3[nH]2)cc1Cl) `ZINC001468268845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468268845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001468268845 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2nc3cc(Cl)c(Cl)cc3[nH]2)cc1Cl NO_LONG_NAME dock atom 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 16, 1, 16, 1, 1, 8, 6, 1, 1, 16, 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, 4, 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] 0 hydrogens 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, 3, 3, 3, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 12, 12, 12, 6, 6, 3, 6, 6, 6, 18, 18, 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268845 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001468268845 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268845/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268845/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468268845 Building ZINC001468449111 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449111' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449111 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468449111 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449111/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449111 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/274 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/274' -> `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)c1ccc(C(F)(F)F)nc1Cl) `ZINC001468449111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468449111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001468449111 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(C(F)(F)F)nc1Cl 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', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'Cl', '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, 1, 5, 15, 15, 15, 8, 1, 16, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 12, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 12, 12, 12, 6, 11, 11, 27, 27] 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]) total number of confs: 82 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449111 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449111/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449111 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 275) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/275 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/275' -> `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)c1ccc(C(F)(F)F)nc1Cl) `ZINC001468449111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468449111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001468449111 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(C(F)(F)F)nc1Cl 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', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'Cl', '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, 1, 5, 15, 15, 15, 8, 1, 16, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 12, 12, 12, 6, 11, 11, 24, 24] 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]) total number of confs: 78 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449111 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001468449111 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449111/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449111/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449111 Building ZINC001468449111 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449111' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449111 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468449111 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449111/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449111 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 274) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(C(F)(F)F)nc1Cl) `ZINC001468449111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468449111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001468449111 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(C(F)(F)F)nc1Cl 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', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'Cl', '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, 1, 5, 15, 15, 15, 8, 1, 16, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 12, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 12, 12, 12, 6, 11, 11, 27, 27] 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]) total number of confs: 82 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449111 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449111/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449111 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 275) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(C(F)(F)F)nc1Cl) `ZINC001468449111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468449111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001468449111 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(C(F)(F)F)nc1Cl 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', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'Cl', '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, 1, 5, 15, 15, 15, 8, 1, 16, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 12, 12, 12, 6, 11, 11, 24, 24] 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]) total number of confs: 78 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449111 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001468449111 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449111/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449111/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449111 Building ZINC001468449112 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449112' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449112 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468449112 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449112/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449112 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/276 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/276' -> `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)c1ccc(C(F)(F)F)nc1Cl) `ZINC001468449112.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468449112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001468449112 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(C(F)(F)F)nc1Cl 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', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'Cl', '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, 1, 5, 15, 15, 15, 8, 1, 16, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 13, 7, 1, 7, 1, 1, 1, 11, 11, 11, 11, 11, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 13, 13, 13, 7, 11, 11, 25, 25] 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]) total number of confs: 80 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449112 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449112/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449112 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 277) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/277 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/277' -> `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)c1ccc(C(F)(F)F)nc1Cl) `ZINC001468449112.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468449112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001468449112 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(C(F)(F)F)nc1Cl 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', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'Cl', '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, 1, 5, 15, 15, 15, 8, 1, 16, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 12, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 12, 12, 12, 6, 11, 11, 27, 27] 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]) total number of confs: 82 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449112 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001468449112 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449112/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449112/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449112 Building ZINC001468449112 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449112' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449112 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468449112 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449112/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449112 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 276) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(C(F)(F)F)nc1Cl) `ZINC001468449112.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468449112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001468449112 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(C(F)(F)F)nc1Cl 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', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'Cl', '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, 1, 5, 15, 15, 15, 8, 1, 16, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 13, 7, 1, 7, 1, 1, 1, 11, 11, 11, 11, 11, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 13, 13, 13, 7, 11, 11, 25, 25] 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]) total number of confs: 80 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449112 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449112/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449112 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 277) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(C(F)(F)F)nc1Cl) `ZINC001468449112.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468449112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001468449112 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(C(F)(F)F)nc1Cl 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', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'Cl', '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, 1, 5, 15, 15, 15, 8, 1, 16, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 12, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 12, 12, 12, 6, 11, 11, 27, 27] 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]) total number of confs: 82 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449112 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001468449112 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449112/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449112/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468449112 Building ZINC001468504094 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468504094' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468504094 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468504094 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468504094/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468504094 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/278 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(c2ccc(OC(F)(F)F)cc2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001468504094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468504094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468504094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001468504094 none O=C(N1CCC(c2ccc(OC(F)(F)F)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', 'O.3', 'C.3', 'F', 'F', 'F', '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, 12, 5, 15, 15, 15, 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, 3, 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, 6, 7, 7, 7, 7, 12, 12, 7, 9, 34, 33, 34, 34, 12, 12, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 12, 12, 12, 12, 7, 7, 7, 7, 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, 47, 48]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468504094 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468504094/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468504094 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 279) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/279 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/279' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(c2ccc(OC(F)(F)F)cc2)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001468504094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468504094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468504094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001468504094 none O=C(N1CCC(c2ccc(OC(F)(F)F)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', 'O.3', 'C.3', 'F', 'F', 'F', '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, 12, 5, 15, 15, 15, 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, 3, 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: [4, 1, 5, 6, 6, 6, 6, 9, 9, 7, 9, 37, 37, 37, 37, 9, 9, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 9, 9, 9, 9, 6, 6, 6, 6, 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, 47, 48]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468504094 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001468504094 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468504094/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468504094/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468504094 Building ZINC001468504094 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468504094' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468504094 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468504094 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468504094/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468504094 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 278) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(N1CCC(c2ccc(OC(F)(F)F)cc2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001468504094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468504094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468504094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001468504094 none O=C(N1CCC(c2ccc(OC(F)(F)F)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', 'O.3', 'C.3', 'F', 'F', 'F', '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, 12, 5, 15, 15, 15, 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, 3, 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, 6, 7, 7, 7, 7, 12, 12, 7, 9, 34, 33, 34, 34, 12, 12, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 12, 12, 12, 12, 7, 7, 7, 7, 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, 47, 48]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468504094 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468504094/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468504094 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 279) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(N1CCC(c2ccc(OC(F)(F)F)cc2)CC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001468504094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468504094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468504094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001468504094 none O=C(N1CCC(c2ccc(OC(F)(F)F)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', 'O.3', 'C.3', 'F', 'F', 'F', '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, 12, 5, 15, 15, 15, 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, 3, 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: [4, 1, 5, 6, 6, 6, 6, 9, 9, 7, 9, 37, 37, 37, 37, 9, 9, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 9, 9, 9, 9, 6, 6, 6, 6, 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, 47, 48]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468504094 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001468504094 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468504094/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468504094/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001468504094 Building ZINC001469231398 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469231398' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469231398 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469231398 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469231398/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469231398 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/280 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C)cc(CNC(=O)OC(C)(C)C)c2)cc1Cl) `ZINC001469231398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469231398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469231398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001469231398 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C)cc(CNC(=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.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', '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, 1, 1, 1, 5, 1, 1, 5, 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: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 2, 6, 6, 14, 24, 33, 33, 33, 33, 33, 33, 6, 4, 4, 4, 6, 6, 6, 4, 4, 2, 6, 6, 6, 6, 3, 14, 14, 24, 33, 33, 33, 33, 33, 33, 33, 33, 33, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469231398 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469231398/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469231398 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 281) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/281 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/281' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C)cc(CNC(=O)OC(C)(C)C)c2)cc1Cl) `ZINC001469231398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469231398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469231398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001469231398 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C)cc(CNC(=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.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', '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, 1, 1, 1, 5, 1, 1, 5, 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: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 2, 6, 6, 12, 23, 31, 31, 31, 31, 31, 31, 6, 4, 4, 4, 6, 6, 6, 4, 4, 2, 6, 6, 6, 6, 2, 12, 12, 23, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469231398 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001469231398 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469231398/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469231398/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469231398 Building ZINC001469231398 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469231398' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469231398 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469231398 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469231398/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469231398 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 280) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C)cc(CNC(=O)OC(C)(C)C)c2)cc1Cl) `ZINC001469231398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469231398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469231398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001469231398 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C)cc(CNC(=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.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', '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, 1, 1, 1, 5, 1, 1, 5, 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: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 2, 6, 6, 14, 24, 33, 33, 33, 33, 33, 33, 6, 4, 4, 4, 6, 6, 6, 4, 4, 2, 6, 6, 6, 6, 3, 14, 14, 24, 33, 33, 33, 33, 33, 33, 33, 33, 33, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469231398 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469231398/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469231398 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 281) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C)cc(CNC(=O)OC(C)(C)C)c2)cc1Cl) `ZINC001469231398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469231398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469231398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001469231398 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C)cc(CNC(=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.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', '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, 1, 1, 1, 5, 1, 1, 5, 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: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 2, 6, 6, 12, 23, 31, 31, 31, 31, 31, 31, 6, 4, 4, 4, 6, 6, 6, 4, 4, 2, 6, 6, 6, 6, 2, 12, 12, 23, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469231398 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001469231398 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469231398/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469231398/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469231398 Building ZINC001469377404 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377404' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377404 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469377404 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377404/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377404 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/282 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCc2[nH]c3ccc(Cl)cc3c2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001469377404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469377404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001469377404 none O=C(N[C@H]1CCc2[nH]c3ccc(Cl)cc3c2C1)[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', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 8, 6, 1, 1, 1, 1, 16, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens 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, 10, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 11, 11, 11, 11, 11, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 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, 38]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377404 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377404/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377404 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 283) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/283 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/283' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCc2[nH]c3ccc(Cl)cc3c2C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001469377404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469377404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001469377404 none O=C(N[C@H]1CCc2[nH]c3ccc(Cl)cc3c2C1)[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', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 8, 6, 1, 1, 1, 1, 16, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens 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, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 10, 10, 10, 10, 10, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 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, 38]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377404 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001469377404 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377404/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377404/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377404 Building ZINC001469377404 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377404' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377404 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469377404 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377404/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377404 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 282) grep: /scratch/xiaobo/12845/xbi-8058088.35/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]1CCc2[nH]c3ccc(Cl)cc3c2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001469377404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469377404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001469377404 none O=C(N[C@H]1CCc2[nH]c3ccc(Cl)cc3c2C1)[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', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 8, 6, 1, 1, 1, 1, 16, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens 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, 10, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 11, 11, 11, 11, 11, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 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, 38]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377404 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377404/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377404 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 283) grep: /scratch/xiaobo/12845/xbi-8058088.35/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]1CCc2[nH]c3ccc(Cl)cc3c2C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001469377404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469377404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001469377404 none O=C(N[C@H]1CCc2[nH]c3ccc(Cl)cc3c2C1)[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', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 8, 6, 1, 1, 1, 1, 16, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens 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, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 10, 10, 10, 10, 10, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 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, 38]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377404 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001469377404 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377404/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377404/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377404 Building ZINC001469377405 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377405' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377405 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469377405 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377405/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377405 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/284 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCc2[nH]c3ccc(Cl)cc3c2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001469377405.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469377405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001469377405 none O=C(N[C@@H]1CCc2[nH]c3ccc(Cl)cc3c2C1)[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', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 8, 6, 1, 1, 1, 1, 16, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens 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, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 9, 9, 9, 9, 9, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377405 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377405/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377405 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 285) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/285 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/285' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCc2[nH]c3ccc(Cl)cc3c2C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001469377405.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469377405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001469377405 none O=C(N[C@@H]1CCc2[nH]c3ccc(Cl)cc3c2C1)[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', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 8, 6, 1, 1, 1, 1, 16, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens 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, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 10, 10, 10, 10, 10, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 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, 38]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377405 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001469377405 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377405/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377405/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377405 Building ZINC001469377405 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377405' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377405 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469377405 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377405/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377405 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 284) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(N[C@@H]1CCc2[nH]c3ccc(Cl)cc3c2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001469377405.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469377405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001469377405 none O=C(N[C@@H]1CCc2[nH]c3ccc(Cl)cc3c2C1)[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', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 8, 6, 1, 1, 1, 1, 16, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens 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, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 9, 9, 9, 9, 9, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377405 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377405/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377405 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 285) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(N[C@@H]1CCc2[nH]c3ccc(Cl)cc3c2C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001469377405.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469377405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001469377405 none O=C(N[C@@H]1CCc2[nH]c3ccc(Cl)cc3c2C1)[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', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 8, 6, 1, 1, 1, 1, 16, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens 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, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 10, 10, 10, 10, 10, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 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, 38]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377405 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001469377405 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377405/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377405/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469377405 Building ZINC001469653622 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469653622' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469653622 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469653622 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469653622/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469653622 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/286 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/286' -> `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(C)(C)C)c2O)cc1Cl) `ZINC001469653622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469653622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469653622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001469653622 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)cc(C(C)(C)C)c2O)cc1Cl NO_LONG_NAME dock atom 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', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.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, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 1, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [12, 6, 3, 6, 6, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 10, 14, 14, 14, 14, 14, 14, 14, 6, 6, 6, 12, 12, 12, 6, 6, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 28, 6] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 101 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469653622 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469653622/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469653622 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 287) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/287 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/287' -> `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(C)(C)C)c2O)cc1Cl) `ZINC001469653622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469653622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469653622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001469653622 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)cc(C(C)(C)C)c2O)cc1Cl NO_LONG_NAME dock atom 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', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.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, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 1, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [10, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 4, 14, 14, 14, 14, 14, 14, 14, 6, 6, 6, 10, 10, 10, 6, 6, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 28, 6] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469653622 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001469653622 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469653622/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469653622/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469653622 Building ZINC001469653622 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469653622' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469653622 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469653622 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469653622/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469653622 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 286) grep: /scratch/xiaobo/12845/xbi-8058088.35/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@]([O-])([SiH3])C(=O)Nc2cc(Br)cc(C(C)(C)C)c2O)cc1Cl) `ZINC001469653622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469653622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469653622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001469653622 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)cc(C(C)(C)C)c2O)cc1Cl NO_LONG_NAME dock atom 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', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.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, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 1, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [12, 6, 3, 6, 6, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 10, 14, 14, 14, 14, 14, 14, 14, 6, 6, 6, 12, 12, 12, 6, 6, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 28, 6] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 101 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469653622 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469653622/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469653622 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 287) grep: /scratch/xiaobo/12845/xbi-8058088.35/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@@]([O-])([SiH3])C(=O)Nc2cc(Br)cc(C(C)(C)C)c2O)cc1Cl) `ZINC001469653622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469653622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469653622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001469653622 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)cc(C(C)(C)C)c2O)cc1Cl NO_LONG_NAME dock atom 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', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.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, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 1, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [10, 6, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 4, 14, 14, 14, 14, 14, 14, 14, 6, 6, 6, 10, 10, 10, 6, 6, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 28, 6] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469653622 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001469653622 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469653622/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469653622/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469653622 Building ZINC001469758625 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469758625' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469758625 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469758625 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469758625/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469758625 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/288 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(Sc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)nc2)c1) `ZINC001469758625.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469758625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469758625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001469758625 none COc1cccc(Sc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)nc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', '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', 'C.2', 'C.2', 'Br', 'S.3', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 8, 1, 1, 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, 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] 0 hydrogens 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, 22, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 50, 50, 50, 50, 50, 50, 50, 4, 4, 2, 3, 3, 4, 50] 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469758625 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469758625/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469758625 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 289) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/289 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/289' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(Sc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)nc2)c1) `ZINC001469758625.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469758625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469758625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001469758625 none COc1cccc(Sc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)nc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', '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', 'C.2', 'C.2', 'Br', 'S.3', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 8, 1, 1, 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, 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] 0 hydrogens 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, 49, 49, 49, 49, 22, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 49, 50, 50, 50, 49, 49, 49, 4, 4, 2, 2, 2, 4, 49] 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469758625 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001469758625 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469758625/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469758625/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469758625 Building ZINC001469758625 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469758625' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469758625 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469758625 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469758625/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469758625 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 288) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1cccc(Sc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)nc2)c1) `ZINC001469758625.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469758625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469758625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001469758625 none COc1cccc(Sc2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)nc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', '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', 'C.2', 'C.2', 'Br', 'S.3', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 8, 1, 1, 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, 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] 0 hydrogens 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, 22, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 50, 50, 50, 50, 50, 50, 50, 4, 4, 2, 3, 3, 4, 50] 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469758625 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469758625/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469758625 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 289) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1cccc(Sc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)nc2)c1) `ZINC001469758625.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469758625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469758625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001469758625 none COc1cccc(Sc2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)nc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', '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', 'C.2', 'C.2', 'Br', 'S.3', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 8, 1, 1, 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, 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] 0 hydrogens 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, 49, 49, 49, 49, 22, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 49, 50, 50, 50, 49, 49, 49, 4, 4, 2, 2, 2, 4, 49] 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469758625 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001469758625 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469758625/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469758625/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469758625 Building ZINC001469920614 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469920614' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469920614 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469920614 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469920614/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469920614 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/290 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2ccc(Cl)c(Cl)c2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001469920614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469920614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469920614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001469920614 none O=C(N1CCN(c2ccc(Cl)c(Cl)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 8, 1, 1, 1, 1, 16, 1, 16, 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] 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, 7, 7, 7, 7] 0 hydrogens need 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, 9, 16, 16, 16, 16, 46, 46, 39, 46, 46, 46, 46, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 16, 16, 16, 16, 46, 46, 46, 16, 16, 16, 16, 3, 1, 3] 50 rigid atoms, others: [1, 16, 17, 18] 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: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469920614 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469920614/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469920614 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 291) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/291 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/291' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2ccc(Cl)c(Cl)c2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001469920614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469920614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469920614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001469920614 none O=C(N1CCN(c2ccc(Cl)c(Cl)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 8, 1, 1, 1, 1, 16, 1, 16, 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] 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, 7, 7, 7, 7] 0 hydrogens 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, 9, 15, 15, 15, 15, 46, 46, 39, 46, 46, 46, 46, 15, 15, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 15, 15, 46, 46, 46, 15, 15, 15, 15, 3, 1, 3] 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469920614 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001469920614 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469920614/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469920614/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469920614 Building ZINC001469920614 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469920614' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469920614 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469920614 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469920614/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469920614 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 290) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/290: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2ccc(Cl)c(Cl)c2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001469920614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469920614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469920614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001469920614 none O=C(N1CCN(c2ccc(Cl)c(Cl)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 8, 1, 1, 1, 1, 16, 1, 16, 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] 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, 7, 7, 7, 7] 0 hydrogens need 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, 9, 16, 16, 16, 16, 46, 46, 39, 46, 46, 46, 46, 16, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 16, 16, 16, 16, 46, 46, 46, 16, 16, 16, 16, 3, 1, 3] 50 rigid atoms, others: [1, 16, 17, 18] 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: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469920614 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469920614/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469920614 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 291) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/291: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2ccc(Cl)c(Cl)c2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001469920614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469920614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469920614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001469920614 none O=C(N1CCN(c2ccc(Cl)c(Cl)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', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', '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, 8, 1, 1, 1, 1, 16, 1, 16, 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] 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, 7, 7, 7, 7] 0 hydrogens 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, 9, 15, 15, 15, 15, 46, 46, 39, 46, 46, 46, 46, 15, 15, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 15, 15, 15, 15, 46, 46, 46, 15, 15, 15, 15, 3, 1, 3] 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469920614 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001469920614 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469920614/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469920614/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001469920614 Building ZINC001470003948 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470003948' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470003948 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001470003948 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470003948/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470003948 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/292 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCCN(Cc1ccc(Cl)cc1)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001470003948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470003948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470003948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001470003948 none CCN(CC)CCCN(Cc1ccc(Cl)cc1)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 16, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 11, 23, 25, 7, 4, 2, 1, 2, 4, 5, 5, 4, 4, 5, 5, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 11, 11, 8, 8, 4, 4, 4, 4, 5, 5, 5, 5, 4, 4, 4, 4] 50 rigid atoms, others: [8, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 141 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470003948 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470003948/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470003948 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 293) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/293 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/293' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCCN(Cc1ccc(Cl)cc1)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001470003948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470003948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470003948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001470003948 none CCN(CC)CCCN(Cc1ccc(Cl)cc1)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 16, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 11, 23, 24, 7, 4, 2, 1, 2, 4, 5, 5, 4, 4, 5, 5, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 11, 11, 8, 8, 4, 4, 4, 4, 5, 5, 5, 5, 3, 3, 3, 3] 50 rigid atoms, others: [8, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 126 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470003948 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001470003948 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470003948/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470003948/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470003948 Building ZINC001470003948 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470003948' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470003948 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001470003948 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470003948/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470003948 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 292) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/292: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCCN(Cc1ccc(Cl)cc1)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001470003948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470003948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470003948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001470003948 none CCN(CC)CCCN(Cc1ccc(Cl)cc1)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 16, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 11, 23, 25, 7, 4, 2, 1, 2, 4, 5, 5, 4, 4, 5, 5, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 11, 11, 8, 8, 4, 4, 4, 4, 5, 5, 5, 5, 4, 4, 4, 4] 50 rigid atoms, others: [8, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 141 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470003948 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470003948/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470003948 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 293) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/293: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCCN(Cc1ccc(Cl)cc1)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001470003948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470003948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470003948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001470003948 none CCN(CC)CCCN(Cc1ccc(Cl)cc1)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 16, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 11, 23, 24, 7, 4, 2, 1, 2, 4, 5, 5, 4, 4, 5, 5, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 11, 11, 8, 8, 4, 4, 4, 4, 5, 5, 5, 5, 3, 3, 3, 3] 50 rigid atoms, others: [8, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 126 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470003948 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001470003948 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470003948/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470003948/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470003948 Building ZINC001470593072 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470593072' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470593072 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001470593072 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470593072/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470593072 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/294 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1csc(Cc2ccc(Cl)cc2)n1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001470593072.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470593072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470593072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001470593072 none O=C(NCc1csc(Cc2ccc(Cl)cc2)n1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 14, 1, 5, 1, 1, 1, 1, 16, 1, 1, 8, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 13, 22, 22, 22, 22, 34, 35, 35, 34, 34, 35, 35, 22, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 22, 34, 34, 35, 35, 35, 35, 4, 4, 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, 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/12845/xbi-8058088.35/working/building/ZINC001470593072 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470593072/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470593072 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 295) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/295 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/295' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1csc(Cc2ccc(Cl)cc2)n1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001470593072.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470593072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470593072/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001470593072 none O=C(NCc1csc(Cc2ccc(Cl)cc2)n1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 14, 1, 5, 1, 1, 1, 1, 16, 1, 1, 8, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 22, 22, 22, 22, 35, 36, 36, 35, 35, 36, 36, 22, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 12, 12, 22, 35, 35, 36, 36, 36, 36, 4, 4, 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, 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/12845/xbi-8058088.35/working/building/ZINC001470593072 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001470593072 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470593072/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470593072/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470593072 Building ZINC001470593072 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470593072' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470593072 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001470593072 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470593072/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470593072 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 294) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NCc1csc(Cc2ccc(Cl)cc2)n1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001470593072.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470593072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470593072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001470593072 none O=C(NCc1csc(Cc2ccc(Cl)cc2)n1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 14, 1, 5, 1, 1, 1, 1, 16, 1, 1, 8, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 13, 22, 22, 22, 22, 34, 35, 35, 34, 34, 35, 35, 22, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 22, 34, 34, 35, 35, 35, 35, 4, 4, 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, 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/12845/xbi-8058088.35/working/building/ZINC001470593072 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470593072/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470593072 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 295) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NCc1csc(Cc2ccc(Cl)cc2)n1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001470593072.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470593072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470593072/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001470593072 none O=C(NCc1csc(Cc2ccc(Cl)cc2)n1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 14, 1, 5, 1, 1, 1, 1, 16, 1, 1, 8, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 12, 22, 22, 22, 22, 35, 36, 36, 35, 35, 36, 36, 22, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 12, 12, 22, 35, 35, 36, 36, 36, 36, 4, 4, 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, 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/12845/xbi-8058088.35/working/building/ZINC001470593072 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001470593072 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470593072/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470593072/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470593072 Building ZINC001470871354 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470871354' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470871354 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001470871354 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470871354/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470871354 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/296 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(Cc2ccccc2Br)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470871354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470871354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470871354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001470871354 none O=C(N1CC(Cc2ccccc2Br)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 1, 1, 1, 1, 1, 1, 17, 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] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 13, 13, 13, 32, 49, 49, 42, 49, 49, 49, 13, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 13, 13, 13, 32, 32, 49, 49, 45, 49, 13, 13, 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: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470871354 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470871354/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470871354 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 297) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/297 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/297' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(Cc2ccccc2Br)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470871354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470871354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470871354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001470871354 none O=C(N1CC(Cc2ccccc2Br)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 1, 1, 1, 1, 1, 1, 17, 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] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 13, 13, 13, 29, 50, 50, 40, 50, 50, 50, 13, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 13, 13, 13, 29, 29, 50, 50, 42, 50, 13, 13, 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/12845/xbi-8058088.35/working/building/ZINC001470871354 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001470871354 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470871354/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470871354/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470871354 Building ZINC001470871354 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470871354' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470871354 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001470871354 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470871354/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470871354 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 296) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CC(Cc2ccccc2Br)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470871354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470871354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470871354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001470871354 none O=C(N1CC(Cc2ccccc2Br)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 1, 1, 1, 1, 1, 1, 17, 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] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 13, 13, 13, 32, 49, 49, 42, 49, 49, 49, 13, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 13, 13, 13, 32, 32, 49, 49, 45, 49, 13, 13, 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: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470871354 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470871354/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470871354 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 297) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CC(Cc2ccccc2Br)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470871354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470871354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470871354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001470871354 none O=C(N1CC(Cc2ccccc2Br)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 1, 1, 1, 1, 1, 1, 17, 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] 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 13, 13, 13, 29, 50, 50, 40, 50, 50, 50, 13, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 13, 13, 13, 29, 29, 50, 50, 42, 50, 13, 13, 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/12845/xbi-8058088.35/working/building/ZINC001470871354 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001470871354 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470871354/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470871354/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001470871354 Building ZINC001471268753 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471268753' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471268753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471268753 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471268753/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471268753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/298 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc3ccn(Cc4ccc(CO)cc4)c3c2)cc1Cl) `ZINC001471268753.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471268753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471268753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001471268753 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc3ccn(Cc4ccc(CO)cc4)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', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 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: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 15, 15, 15, 15, 15, 28, 15, 15, 7, 7, 4, 4, 4, 8, 8, 8, 4, 4, 2, 7, 7, 7, 7, 15, 15, 15, 15, 28, 28, 84, 15, 15, 7, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471268753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471268753/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471268753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 299) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/299 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/299' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc3ccn(Cc4ccc(CO)cc4)c3c2)cc1Cl) `ZINC001471268753.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471268753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471268753/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001471268753 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc3ccn(Cc4ccc(CO)cc4)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', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 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: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 16, 16, 16, 16, 16, 29, 16, 16, 7, 7, 4, 4, 4, 8, 8, 8, 4, 4, 2, 7, 7, 7, 7, 16, 16, 16, 16, 29, 29, 87, 16, 16, 7, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471268753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001471268753 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471268753/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471268753/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471268753 Building ZINC001471268753 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471268753' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471268753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471268753 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471268753/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471268753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 298) grep: /scratch/xiaobo/12845/xbi-8058088.35/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([C@@]([O-])([SiH3])C(=O)Nc2ccc3ccn(Cc4ccc(CO)cc4)c3c2)cc1Cl) `ZINC001471268753.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471268753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471268753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001471268753 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc3ccn(Cc4ccc(CO)cc4)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', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 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: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 15, 15, 15, 15, 15, 28, 15, 15, 7, 7, 4, 4, 4, 8, 8, 8, 4, 4, 2, 7, 7, 7, 7, 15, 15, 15, 15, 28, 28, 84, 15, 15, 7, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471268753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471268753/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471268753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 299) grep: /scratch/xiaobo/12845/xbi-8058088.35/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([C@]([O-])([SiH3])C(=O)Nc2ccc3ccn(Cc4ccc(CO)cc4)c3c2)cc1Cl) `ZINC001471268753.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471268753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471268753/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001471268753 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc3ccn(Cc4ccc(CO)cc4)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', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 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: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 16, 16, 16, 16, 16, 29, 16, 16, 7, 7, 4, 4, 4, 8, 8, 8, 4, 4, 2, 7, 7, 7, 7, 16, 16, 16, 16, 29, 29, 87, 16, 16, 7, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471268753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001471268753 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471268753/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471268753/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471268753 Building ZINC001471773475 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471773475' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471773475 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471773475 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471773475/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471773475 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/300 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc(Br)c2ccccc2c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471773475.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471773475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471773475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001471773475 none O=C(NCc1cc(Br)c2ccccc2c1)[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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 17, 1, 1, 1, 1, 1, 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] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 11, 31, 31, 31, 31, 31, 31, 31, 31, 31, 28, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 31, 31, 31, 31, 31, 31, 4, 4, 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, 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/12845/xbi-8058088.35/working/building/ZINC001471773475 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471773475/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471773475 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 301) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/301 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/301' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc(Br)c2ccccc2c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471773475.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471773475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471773475/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001471773475 none O=C(NCc1cc(Br)c2ccccc2c1)[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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 17, 1, 1, 1, 1, 1, 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] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 11, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 31, 31, 31, 31, 31, 31, 4, 4, 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, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471773475 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001471773475 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471773475/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471773475/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471773475 Building ZINC001471773475 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471773475' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471773475 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471773475 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471773475/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471773475 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 300) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(NCc1cc(Br)c2ccccc2c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471773475.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471773475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471773475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001471773475 none O=C(NCc1cc(Br)c2ccccc2c1)[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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 17, 1, 1, 1, 1, 1, 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] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 11, 31, 31, 31, 31, 31, 31, 31, 31, 31, 28, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 31, 31, 31, 31, 31, 31, 4, 4, 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, 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/12845/xbi-8058088.35/working/building/ZINC001471773475 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471773475/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471773475 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 301) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(NCc1cc(Br)c2ccccc2c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471773475.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471773475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471773475/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001471773475 none O=C(NCc1cc(Br)c2ccccc2c1)[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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 17, 1, 1, 1, 1, 1, 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] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 11, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 31, 31, 31, 31, 31, 31, 4, 4, 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, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471773475 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001471773475 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471773475/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471773475/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471773475 Building ZINC001471803757 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471803757' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471803757 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471803757 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471803757/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471803757 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/302 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc(C(F)(F)F)ccc1Br)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471803757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471803757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471803757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001471803757 none O=C(NCc1cc(C(F)(F)F)ccc1Br)[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', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 15, 15, 15, 1, 1, 1, 17, 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, 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, 30, 30, 30, 30, 30, 30, 21, 30, 30, 30, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 30, 30, 30, 4, 4, 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, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471803757 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471803757/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471803757 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 303) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/303 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/303' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc(C(F)(F)F)ccc1Br)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471803757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471803757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471803757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001471803757 none O=C(NCc1cc(C(F)(F)F)ccc1Br)[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', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 15, 15, 15, 1, 1, 1, 17, 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, 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, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 31, 31, 31, 4, 4, 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, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471803757 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001471803757 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471803757/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471803757/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471803757 Building ZINC001471803757 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471803757' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471803757 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471803757 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471803757/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471803757 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 302) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NCc1cc(C(F)(F)F)ccc1Br)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471803757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471803757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471803757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001471803757 none O=C(NCc1cc(C(F)(F)F)ccc1Br)[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', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 15, 15, 15, 1, 1, 1, 17, 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, 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, 30, 30, 30, 30, 30, 30, 21, 30, 30, 30, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 30, 30, 30, 4, 4, 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, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471803757 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471803757/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471803757 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 303) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NCc1cc(C(F)(F)F)ccc1Br)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471803757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471803757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471803757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001471803757 none O=C(NCc1cc(C(F)(F)F)ccc1Br)[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', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 15, 15, 15, 1, 1, 1, 17, 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, 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, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 16, 16, 31, 31, 31, 4, 4, 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, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471803757 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001471803757 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471803757/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471803757/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471803757 Building ZINC001471880060 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880060' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880060 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471880060 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880060/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880060 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/304 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)CC[C@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001471880060.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471880060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001471880060 none CC(C)(C)OC(=O)CC[C@H]1Cc2ccccc2N(C(=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.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.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 42, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 8, 8, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [50, 51, 52, 21, 22, 23, 24, 25, 26, 27, 28, 29, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 54, 55]) total number of confs: 140 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880060 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880060/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880060 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 305) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/305 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/305' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)CC[C@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001471880060.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471880060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880060/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001471880060 none CC(C)(C)OC(=O)CC[C@H]1Cc2ccccc2N(C(=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.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.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 11, 43, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 7, 7, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [50, 51, 52, 21, 22, 23, 24, 25, 26, 27, 28, 29, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 54, 55]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880060 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001471880060 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880060/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880060/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880060 Building ZINC001471880060 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880060' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880060 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471880060 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880060/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880060 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 304) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)OC(=O)CC[C@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001471880060.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471880060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001471880060 none CC(C)(C)OC(=O)CC[C@H]1Cc2ccccc2N(C(=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.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.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 42, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 8, 8, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [50, 51, 52, 21, 22, 23, 24, 25, 26, 27, 28, 29, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 54, 55]) total number of confs: 140 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880060 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880060/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880060 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 305) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)OC(=O)CC[C@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001471880060.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471880060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880060/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001471880060 none CC(C)(C)OC(=O)CC[C@H]1Cc2ccccc2N(C(=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.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.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 11, 43, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 7, 7, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [50, 51, 52, 21, 22, 23, 24, 25, 26, 27, 28, 29, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 54, 55]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880060 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001471880060 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880060/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880060/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880060 Building ZINC001471880062 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880062' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880062 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471880062 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880062/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880062 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/306 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)CC[C@@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001471880062.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471880062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001471880062 none CC(C)(C)OC(=O)CC[C@@H]1Cc2ccccc2N(C(=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.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.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 12, 43, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 10, 10, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [50, 51, 52, 21, 22, 23, 24, 25, 26, 27, 28, 29, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 54, 55]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880062 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880062/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880062 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 307) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/307 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/307' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)CC[C@@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001471880062.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471880062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880062/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001471880062 none CC(C)(C)OC(=O)CC[C@@H]1Cc2ccccc2N(C(=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.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.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 13, 45, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 9, 9, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [50, 51, 52, 21, 22, 23, 24, 25, 26, 27, 28, 29, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 54, 55]) total number of confs: 149 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880062 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001471880062 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880062/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880062/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880062 Building ZINC001471880062 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880062' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880062 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471880062 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880062/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880062 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 306) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)OC(=O)CC[C@@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001471880062.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471880062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001471880062 none CC(C)(C)OC(=O)CC[C@@H]1Cc2ccccc2N(C(=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.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.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 12, 43, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 10, 10, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [50, 51, 52, 21, 22, 23, 24, 25, 26, 27, 28, 29, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 54, 55]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880062 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880062/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880062 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 307) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)OC(=O)CC[C@@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C1) `ZINC001471880062.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471880062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880062/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001471880062 none CC(C)(C)OC(=O)CC[C@@H]1Cc2ccccc2N(C(=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.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.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 13, 45, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 9, 9, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [50, 51, 52, 21, 22, 23, 24, 25, 26, 27, 28, 29, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 54, 55]) total number of confs: 149 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880062 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001471880062 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880062/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880062/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471880062 Building ZINC001471935114 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471935114' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471935114 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471935114 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471935114/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471935114 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/308 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(F)ccc1Oc1ccc(Br)cc1)C(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC001471935114.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471935114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471935114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001471935114 none CN(Cc1cc(F)ccc1Oc1ccc(Br)cc1)C(=O)[C@]([O-])([SiH3])c1cccn1C 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', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 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: [5, 2, 5, 17, 26, 26, 26, 26, 26, 26, 26, 48, 48, 48, 48, 48, 48, 48, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 5, 17, 17, 26, 17, 26, 48, 48, 48, 48, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471935114 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471935114/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471935114 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 309) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/309 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/309' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(F)ccc1Oc1ccc(Br)cc1)C(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC001471935114.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471935114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471935114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001471935114 none CN(Cc1cc(F)ccc1Oc1ccc(Br)cc1)C(=O)[C@@]([O-])([SiH3])c1cccn1C 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', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 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: [5, 2, 5, 16, 24, 24, 24, 24, 24, 24, 24, 48, 48, 48, 48, 48, 48, 48, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 5, 16, 16, 24, 16, 24, 48, 48, 48, 48, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471935114 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001471935114 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471935114/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471935114/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471935114 Building ZINC001471935114 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471935114' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471935114 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471935114 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471935114/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471935114 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 308) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CN(Cc1cc(F)ccc1Oc1ccc(Br)cc1)C(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC001471935114.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471935114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471935114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001471935114 none CN(Cc1cc(F)ccc1Oc1ccc(Br)cc1)C(=O)[C@]([O-])([SiH3])c1cccn1C 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', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 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: [5, 2, 5, 17, 26, 26, 26, 26, 26, 26, 26, 48, 48, 48, 48, 48, 48, 48, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 5, 17, 17, 26, 17, 26, 48, 48, 48, 48, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471935114 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471935114/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471935114 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 309) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CN(Cc1cc(F)ccc1Oc1ccc(Br)cc1)C(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC001471935114.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471935114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471935114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001471935114 none CN(Cc1cc(F)ccc1Oc1ccc(Br)cc1)C(=O)[C@@]([O-])([SiH3])c1cccn1C 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', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 15, 1, 1, 1, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 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: [5, 2, 5, 16, 24, 24, 24, 24, 24, 24, 24, 48, 48, 48, 48, 48, 48, 48, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 5, 16, 16, 24, 16, 24, 48, 48, 48, 48, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471935114 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001471935114 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471935114/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471935114/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471935114 Building ZINC001471993201 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993201' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471993201 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993201/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/310 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](CNc2ccc(Cl)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001471993201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471993201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001471993201 none O=C(N1CCC[C@H](CNc2ccc(Cl)cc2)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.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 5, 6, 6, 6, 6, 6, 6, 19, 33, 36, 36, 33, 33, 36, 36, 6, 1, 1, 1, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 19, 19, 33, 36, 36, 36, 36, 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, 42]) total number of confs: 131 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993201/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 311) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/311 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/311' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](CNc2ccc(Cl)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001471993201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471993201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001471993201 none O=C(N1CCC[C@H](CNc2ccc(Cl)cc2)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.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 7, 9, 9, 9, 9, 9, 9, 24, 35, 36, 36, 35, 35, 36, 36, 9, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 24, 24, 35, 36, 36, 36, 36, 9, 9, 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, 42]) total number of confs: 123 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001471993201 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993201/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993201/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993201 Building ZINC001471993201 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993201' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471993201 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993201/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 310) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(N1CCC[C@H](CNc2ccc(Cl)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001471993201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471993201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001471993201 none O=C(N1CCC[C@H](CNc2ccc(Cl)cc2)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.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 5, 6, 6, 6, 6, 6, 6, 19, 33, 36, 36, 33, 33, 36, 36, 6, 1, 1, 1, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 19, 19, 33, 36, 36, 36, 36, 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, 42]) total number of confs: 131 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993201/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 311) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(N1CCC[C@H](CNc2ccc(Cl)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001471993201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471993201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001471993201 none O=C(N1CCC[C@H](CNc2ccc(Cl)cc2)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.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 7, 9, 9, 9, 9, 9, 9, 24, 35, 36, 36, 35, 35, 36, 36, 9, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 24, 24, 35, 36, 36, 36, 36, 9, 9, 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, 42]) total number of confs: 123 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001471993201 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993201/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993201/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993201 Building ZINC001471993202 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993202' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993202 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471993202 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993202/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993202 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/312 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](CNc2ccc(Cl)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001471993202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471993202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001471993202 none O=C(N1CCC[C@@H](CNc2ccc(Cl)cc2)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.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 7, 9, 9, 9, 9, 9, 9, 24, 35, 36, 36, 35, 35, 36, 36, 9, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 24, 24, 35, 36, 36, 36, 36, 9, 9, 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, 42]) total number of confs: 123 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993202 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993202/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993202 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 313) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/313 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/313' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](CNc2ccc(Cl)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001471993202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471993202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001471993202 none O=C(N1CCC[C@@H](CNc2ccc(Cl)cc2)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.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 5, 6, 6, 6, 6, 6, 6, 19, 33, 36, 36, 33, 33, 36, 36, 6, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 19, 19, 33, 36, 36, 36, 36, 6, 6, 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, 42]) total number of confs: 128 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993202 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001471993202 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993202/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993202/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993202 Building ZINC001471993202 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993202' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993202 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471993202 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993202/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993202 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 312) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CCC[C@@H](CNc2ccc(Cl)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001471993202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471993202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001471993202 none O=C(N1CCC[C@@H](CNc2ccc(Cl)cc2)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.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 7, 9, 9, 9, 9, 9, 9, 24, 35, 36, 36, 35, 35, 36, 36, 9, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 24, 24, 35, 36, 36, 36, 36, 9, 9, 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, 42]) total number of confs: 123 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993202 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993202/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993202 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 313) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CCC[C@@H](CNc2ccc(Cl)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001471993202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471993202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001471993202 none O=C(N1CCC[C@@H](CNc2ccc(Cl)cc2)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.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 5, 6, 6, 6, 6, 6, 6, 19, 33, 36, 36, 33, 33, 36, 36, 6, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 19, 19, 33, 36, 36, 36, 36, 6, 6, 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, 42]) total number of confs: 128 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993202 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001471993202 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993202/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993202/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001471993202 Building ZINC001472070746 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070746' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070746 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472070746 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070746/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070746 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/314 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21) `ZINC001472070746.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472070746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001472070746 none CC(C)(C)OC(=O)NCC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 36, 25, 36, 12, 8, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 12, 12, 8, 8, 3, 3, 2, 2, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070746 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070746/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070746 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 315) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/315 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/315' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21) `ZINC001472070746.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472070746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070746/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001472070746 none CC(C)(C)OC(=O)NCC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 36, 28, 36, 9, 6, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 37, 37, 37, 37, 37, 37, 37, 37, 37, 28, 9, 9, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070746 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472070746 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070746/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070746/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070746 Building ZINC001472070746 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070746' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070746 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472070746 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070746/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070746 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 314) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)OC(=O)NCC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21) `ZINC001472070746.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472070746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001472070746 none CC(C)(C)OC(=O)NCC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 36, 25, 36, 12, 8, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 37, 37, 37, 37, 37, 37, 37, 37, 37, 25, 12, 12, 8, 8, 3, 3, 2, 2, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070746 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070746/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070746 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 315) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)OC(=O)NCC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21) `ZINC001472070746.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472070746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070746/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001472070746 none CC(C)(C)OC(=O)NCC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 36, 28, 36, 9, 6, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 37, 37, 37, 37, 37, 37, 37, 37, 37, 28, 9, 9, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070746 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472070746 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070746/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070746/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070746 Building ZINC001472070747 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070747' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070747 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472070747 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070747/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070747 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/316 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21) `ZINC001472070747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472070747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001472070747 none CC(C)(C)OC(=O)NCC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 32, 26, 32, 8, 6, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 33, 33, 33, 33, 33, 33, 33, 33, 33, 26, 8, 8, 6, 6, 3, 3, 2, 2, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070747 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070747/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070747 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 317) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/317 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/317' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21) `ZINC001472070747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472070747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001472070747 none CC(C)(C)OC(=O)NCC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 34, 24, 34, 11, 7, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 36, 36, 36, 36, 36, 36, 36, 36, 36, 24, 11, 11, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070747 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472070747 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070747/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070747/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070747 Building ZINC001472070747 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070747' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070747 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472070747 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070747/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070747 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 316) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)OC(=O)NCC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21) `ZINC001472070747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472070747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001472070747 none CC(C)(C)OC(=O)NCC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 32, 26, 32, 8, 6, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 33, 33, 33, 33, 33, 33, 33, 33, 33, 26, 8, 8, 6, 6, 3, 3, 2, 2, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070747 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070747/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070747 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 317) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)OC(=O)NCC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c2ccccc21) `ZINC001472070747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472070747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001472070747 none CC(C)(C)OC(=O)NCC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)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', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 34, 24, 34, 11, 7, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 36, 36, 36, 36, 36, 36, 36, 36, 36, 24, 11, 11, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070747 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472070747 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070747/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070747/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070747 Building ZINC001472070854 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070854' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070854 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472070854 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070854/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070854 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/318 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc21) `ZINC001472070854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472070854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001472070854 none CC(C)(C)OC(=O)NCC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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, 7] 0 hydrogens 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, 49, 38, 49, 12, 7, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 12, 12, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [48, 49, 50, 14, 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, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52, 53, 54]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070854 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070854/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070854 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 319) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/319 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/319' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc21) `ZINC001472070854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472070854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001472070854 none CC(C)(C)OC(=O)NCC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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, 7] 0 hydrogens 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, 49, 35, 49, 14, 9, 4, 4, 4, 4, 3, 2, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 14, 14, 9, 9, 4, 4, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [48, 49, 50, 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, 43, 44, 45, 46, 51, 52, 53, 54]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070854 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472070854 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070854/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070854/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070854 Building ZINC001472070854 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070854' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070854 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472070854 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070854/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070854 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 318) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)OC(=O)NCC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc21) `ZINC001472070854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472070854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001472070854 none CC(C)(C)OC(=O)NCC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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, 7] 0 hydrogens 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, 49, 38, 49, 12, 7, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 12, 12, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [48, 49, 50, 14, 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, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52, 53, 54]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070854 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070854/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070854 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 319) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)OC(=O)NCC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc21) `ZINC001472070854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472070854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001472070854 none CC(C)(C)OC(=O)NCC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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, 7] 0 hydrogens 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, 49, 35, 49, 14, 9, 4, 4, 4, 4, 3, 2, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 14, 14, 9, 9, 4, 4, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [48, 49, 50, 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, 43, 44, 45, 46, 51, 52, 53, 54]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070854 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472070854 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070854/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070854/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070854 Building ZINC001472070855 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070855' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070855 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472070855 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070855/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070855 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/320 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc21) `ZINC001472070855.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472070855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001472070855 none CC(C)(C)OC(=O)NCC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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, 7] 0 hydrogens 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, 45, 33, 45, 14, 9, 4, 4, 4, 4, 3, 2, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 14, 14, 9, 9, 4, 4, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [48, 49, 50, 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, 43, 44, 45, 46, 51, 52, 53, 54]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070855 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070855/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070855 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 321) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/321 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/321' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc21) `ZINC001472070855.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472070855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070855/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001472070855 none CC(C)(C)OC(=O)NCC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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, 7] 0 hydrogens 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, 47, 38, 47, 12, 7, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 12, 12, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [48, 49, 50, 14, 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, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52, 53, 54]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070855 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472070855 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070855/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070855/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070855 Building ZINC001472070855 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070855' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070855 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472070855 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070855/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070855 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 320) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)OC(=O)NCC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc21) `ZINC001472070855.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472070855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001472070855 none CC(C)(C)OC(=O)NCC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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, 7] 0 hydrogens 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, 45, 33, 45, 14, 9, 4, 4, 4, 4, 3, 2, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 14, 14, 9, 9, 4, 4, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [48, 49, 50, 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, 43, 44, 45, 46, 51, 52, 53, 54]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070855 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070855/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070855 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 321) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)OC(=O)NCC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2ccccc21) `ZINC001472070855.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472070855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070855/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001472070855 none CC(C)(C)OC(=O)NCC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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, 7] 0 hydrogens 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, 47, 38, 47, 12, 7, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 12, 12, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [48, 49, 50, 14, 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, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 51, 52, 53, 54]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070855 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472070855 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070855/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070855/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472070855 Building ZINC001472143463 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472143463' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472143463 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472143463 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472143463/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472143463 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/322 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1c(OCc2ccccc2)ccc2ccccc21)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001472143463.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472143463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472143463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001472143463 none CN(Cc1c(OCc2ccccc2)ccc2ccccc21)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.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, 8, 5, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 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] 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, 6, 9, 9, 26, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9, 9, 9, 9, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 3, 3, 6, 6, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9, 9, 2, 2, 4, 2, 2] 100 rigid atoms, others: [21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472143463 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472143463/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472143463 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 323) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/323 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/323' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1c(OCc2ccccc2)ccc2ccccc21)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001472143463.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472143463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472143463/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001472143463 none CN(Cc1c(OCc2ccccc2)ccc2ccccc21)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.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, 8, 5, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 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] 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, 7, 9, 9, 25, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9, 9, 9, 9, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 4, 4, 7, 7, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9, 9, 2, 2, 4, 2, 2] 100 rigid atoms, others: [21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472143463 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472143463 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472143463/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472143463/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472143463 Building ZINC001472143463 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472143463' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472143463 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472143463 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472143463/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472143463 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 322) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CN(Cc1c(OCc2ccccc2)ccc2ccccc21)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001472143463.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472143463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472143463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001472143463 none CN(Cc1c(OCc2ccccc2)ccc2ccccc21)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.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, 8, 5, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 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] 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, 6, 9, 9, 26, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9, 9, 9, 9, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 3, 3, 6, 6, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9, 9, 2, 2, 4, 2, 2] 100 rigid atoms, others: [21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472143463 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472143463/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472143463 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 323) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CN(Cc1c(OCc2ccccc2)ccc2ccccc21)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001472143463.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472143463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472143463/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001472143463 none CN(Cc1c(OCc2ccccc2)ccc2ccccc21)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.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, 8, 5, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 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] 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, 7, 9, 9, 25, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9, 9, 9, 9, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 4, 4, 7, 7, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9, 9, 2, 2, 4, 2, 2] 100 rigid atoms, others: [21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472143463 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472143463 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472143463/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472143463/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472143463 Building ZINC001472482073 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472482073' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472482073 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472482073 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472482073/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472482073 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/324 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)Cc1ccc(c2ccccc2CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001472482073.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472482073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472482073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001472482073 none CN(C)Cc1ccc(c2ccccc2CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.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', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 19, 19, 20, 20, 19, 19, 19, 19, 19, 19, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 36, 36, 36, 36, 36, 36, 36, 36, 20, 20, 19, 19, 19, 19, 10, 10, 3, 4, 4, 4, 4, 20, 20] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472482073 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472482073/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472482073 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 325) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/325 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/325' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)Cc1ccc(c2ccccc2CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001472482073.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472482073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472482073/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001472482073 none CN(C)Cc1ccc(c2ccccc2CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.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', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 18, 18, 20, 20, 18, 18, 18, 18, 18, 18, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 35, 35, 35, 35, 35, 35, 35, 35, 20, 20, 18, 18, 18, 18, 11, 11, 3, 4, 4, 4, 4, 20, 20] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472482073 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472482073 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472482073/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472482073/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472482073 Building ZINC001472482073 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472482073' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472482073 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472482073 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472482073/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472482073 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 324) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CN(C)Cc1ccc(c2ccccc2CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001472482073.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472482073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472482073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001472482073 none CN(C)Cc1ccc(c2ccccc2CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.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', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 19, 19, 20, 20, 19, 19, 19, 19, 19, 19, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 36, 36, 36, 36, 36, 36, 36, 36, 20, 20, 19, 19, 19, 19, 10, 10, 3, 4, 4, 4, 4, 20, 20] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472482073 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472482073/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472482073 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 325) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CN(C)Cc1ccc(c2ccccc2CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1) `ZINC001472482073.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472482073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472482073/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001472482073 none CN(C)Cc1ccc(c2ccccc2CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.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.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', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 18, 18, 20, 20, 18, 18, 18, 18, 18, 18, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 35, 35, 35, 35, 35, 35, 35, 35, 20, 20, 18, 18, 18, 18, 11, 11, 3, 4, 4, 4, 4, 20, 20] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472482073 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472482073 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472482073/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472482073/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472482073 Building ZINC001472501316 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472501316' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472501316 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472501316 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472501316/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472501316 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/326 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(c2cc(Br)ccc2Cl)[nH]n1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001472501316.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472501316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472501316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001472501316 none O=C(Nc1cc(c2cc(Br)ccc2Cl)[nH]n1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 16, 8, 6, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 8, 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, 7, 7, 7, 31, 31, 31, 16, 31, 31, 31, 7, 7, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 7, 31, 11, 31, 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472501316 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472501316/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472501316 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 327) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/327 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/327' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(c2cc(Br)ccc2Cl)[nH]n1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001472501316.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472501316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472501316/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001472501316 none O=C(Nc1cc(c2cc(Br)ccc2Cl)[nH]n1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 16, 8, 6, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 8, 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, 7, 7, 7, 30, 30, 30, 17, 30, 30, 30, 7, 7, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 7, 30, 30, 30, 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472501316 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472501316 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472501316/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472501316/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472501316 Building ZINC001472501316 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472501316' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472501316 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472501316 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472501316/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472501316 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 326) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1cc(c2cc(Br)ccc2Cl)[nH]n1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001472501316.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472501316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472501316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001472501316 none O=C(Nc1cc(c2cc(Br)ccc2Cl)[nH]n1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 16, 8, 6, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 8, 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, 7, 7, 7, 31, 31, 31, 16, 31, 31, 31, 7, 7, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 7, 31, 11, 31, 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472501316 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472501316/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472501316 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 327) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1cc(c2cc(Br)ccc2Cl)[nH]n1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001472501316.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472501316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472501316/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001472501316 none O=C(Nc1cc(c2cc(Br)ccc2Cl)[nH]n1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 16, 8, 6, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 8, 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, 7, 7, 7, 30, 30, 30, 17, 30, 30, 30, 7, 7, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 7, 30, 30, 30, 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472501316 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472501316 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472501316/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472501316/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472501316 Building ZINC001472518314 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518314' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518314 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472518314 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518314/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518314 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/328 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)o1) `ZINC001472518314.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472518314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001472518314 none Cc1ccc(CC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 11, 11, 11, 6, 6, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 3, 3, 3, 1, 2, 2, 2, 9, 9, 4, 9, 2, 2, 2] 50 rigid atoms, others: [7, 10, 11, 12, 13, 14, 45, 15] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 59 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518314 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518314/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518314 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 329) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/329 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/329' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CC[C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)o1) `ZINC001472518314.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472518314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518314/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001472518314 none Cc1ccc(CC[C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 13, 13, 13, 6, 6, 4, 1, 4, 4, 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, 6, 6, 6, 6, 4, 4, 4, 1, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2] 50 rigid atoms, others: [7, 10, 11, 12, 13, 14, 45, 15] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518314 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472518314 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518314/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518314/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518314 Building ZINC001472518314 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518314' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518314 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472518314 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518314/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518314 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 328) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc(CC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)o1) `ZINC001472518314.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472518314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001472518314 none Cc1ccc(CC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 11, 11, 11, 6, 6, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 3, 3, 3, 1, 2, 2, 2, 9, 9, 4, 9, 2, 2, 2] 50 rigid atoms, others: [7, 10, 11, 12, 13, 14, 45, 15] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 59 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518314 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518314/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518314 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 329) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc(CC[C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)o1) `ZINC001472518314.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472518314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518314/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001472518314 none Cc1ccc(CC[C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 13, 13, 13, 6, 6, 4, 1, 4, 4, 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, 6, 6, 6, 6, 4, 4, 4, 1, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2] 50 rigid atoms, others: [7, 10, 11, 12, 13, 14, 45, 15] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518314 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472518314 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518314/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518314/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518314 Building ZINC001472518315 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518315' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518315 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472518315 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518315/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518315 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/330 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CC[C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)o1) `ZINC001472518315.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472518315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001472518315 none Cc1ccc(CC[C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 13, 13, 13, 6, 6, 4, 1, 4, 4, 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, 6, 6, 6, 6, 4, 4, 4, 1, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2] 50 rigid atoms, others: [7, 10, 11, 12, 13, 14, 45, 15] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518315 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518315/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518315 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 331) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/331 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/331' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CC[C@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)o1) `ZINC001472518315.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472518315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001472518315 none Cc1ccc(CC[C@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 11, 11, 11, 6, 6, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 3, 3, 3, 1, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2] 50 rigid atoms, others: [7, 10, 11, 12, 13, 14, 45, 15] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 55 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518315 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472518315 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518315/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518315/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518315 Building ZINC001472518315 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518315' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518315 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472518315 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518315/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518315 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 330) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc(CC[C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)o1) `ZINC001472518315.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472518315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001472518315 none Cc1ccc(CC[C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 13, 13, 13, 6, 6, 4, 1, 4, 4, 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, 6, 6, 6, 6, 4, 4, 4, 1, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2] 50 rigid atoms, others: [7, 10, 11, 12, 13, 14, 45, 15] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518315 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518315/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518315 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 331) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc(CC[C@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)o1) `ZINC001472518315.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472518315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001472518315 none Cc1ccc(CC[C@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 11, 11, 11, 6, 6, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 3, 3, 3, 1, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2] 50 rigid atoms, others: [7, 10, 11, 12, 13, 14, 45, 15] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 55 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518315 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472518315 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518315/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518315/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472518315 Building ZINC001472525073 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472525073' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472525073 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472525073 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472525073/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472525073 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/332 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/332' -> `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(CC(C)C)CC1) `ZINC001472525073.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472525073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472525073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472525073 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(CC(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, 21, 21, 4, 21, 21, 21, 21, 21, 21, 4, 4, 1, 1, 1, 1, 3, 5, 8, 8, 8, 8, 14, 14, 14, 8, 8, 4, 4, 4, 21, 21, 4, 21, 4, 4, 4, 8, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 91 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472525073 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472525073/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472525073 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 333) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/333 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/333' -> `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(CC(C)C)CC1) `ZINC001472525073.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472525073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472525073/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472525073 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(CC(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, 18, 18, 3, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 1, 2, 4, 6, 6, 6, 6, 13, 13, 13, 6, 6, 3, 3, 3, 18, 18, 4, 18, 3, 3, 3, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 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, 57, 58]) total number of confs: 88 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472525073 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472525073 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472525073/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472525073/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472525073 Building ZINC001472525073 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472525073' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472525073 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472525073 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472525073/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472525073 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 332) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(CC(C)C)CC1) `ZINC001472525073.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472525073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472525073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472525073 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(CC(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, 21, 21, 4, 21, 21, 21, 21, 21, 21, 4, 4, 1, 1, 1, 1, 3, 5, 8, 8, 8, 8, 14, 14, 14, 8, 8, 4, 4, 4, 21, 21, 4, 21, 4, 4, 4, 8, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 91 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472525073 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472525073/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472525073 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 333) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(CC(C)C)CC1) `ZINC001472525073.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472525073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472525073/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472525073 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(CC(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, 18, 18, 3, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 1, 2, 4, 6, 6, 6, 6, 13, 13, 13, 6, 6, 3, 3, 3, 18, 18, 4, 18, 3, 3, 3, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 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, 57, 58]) total number of confs: 88 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472525073 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472525073 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472525073/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472525073/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472525073 Building ZINC001472538011 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538011' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538011 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472538011 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538011/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538011 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/334 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/334' -> `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)N1C[C@H](C)[C@@H]2CCCC[C@@H]21) `ZINC001472538011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472538011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472538011 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)[C@@H]2CCCC[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', 'H', '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'] dock atom type numbers: [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, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 6, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 22, 22, 3, 22, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 71 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538011 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538011/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538011 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 335) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/335 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/335' -> `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)N1C[C@H](C)[C@@H]2CCCC[C@@H]21) `ZINC001472538011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472538011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472538011 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)[C@@H]2CCCC[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', 'H', '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'] dock atom type numbers: [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, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 3, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 2, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 20, 20, 3, 20, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 69 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538011 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472538011 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538011/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538011/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538011 Building ZINC001472538011 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538011' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538011 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472538011 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538011/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538011 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 334) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)[C@@H]2CCCC[C@@H]21) `ZINC001472538011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472538011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472538011 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)[C@@H]2CCCC[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', 'H', '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'] dock atom type numbers: [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, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 2, 6, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 22, 22, 3, 22, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 71 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538011 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538011/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538011 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 335) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)[C@@H]2CCCC[C@@H]21) `ZINC001472538011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472538011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472538011 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)[C@@H]2CCCC[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', 'H', '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'] dock atom type numbers: [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, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 3, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 2, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 20, 20, 3, 20, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 69 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538011 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472538011 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538011/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538011/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538011 Building ZINC001472538022 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538022' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538022 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472538022 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538022/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538022 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/336 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/336' -> `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)N1C[C@H](C)[C@H]2CCCC[C@@H]21) `ZINC001472538022.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472538022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472538022 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)[C@H]2CCCC[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', 'H', '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'] dock atom type numbers: [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, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 31, 31, 6, 31, 31, 31, 31, 31, 31, 3, 3, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 31, 31, 8, 31, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 83 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538022 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538022/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538022 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 337) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/337 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/337' -> `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)N1C[C@H](C)[C@H]2CCCC[C@@H]21) `ZINC001472538022.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472538022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472538022 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)[C@H]2CCCC[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', 'H', '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'] dock atom type numbers: [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, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 27, 27, 4, 27, 27, 27, 27, 27, 27, 4, 4, 1, 1, 1, 2, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 27, 27, 4, 27, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: 76 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538022 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472538022 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538022/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538022/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538022 Building ZINC001472538022 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538022' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538022 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472538022 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538022/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538022 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 336) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/336: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)[C@H]2CCCC[C@@H]21) `ZINC001472538022.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472538022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472538022 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)[C@H]2CCCC[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', 'H', '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'] dock atom type numbers: [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, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 31, 31, 6, 31, 31, 31, 31, 31, 31, 3, 3, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 31, 31, 8, 31, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 83 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538022 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538022/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538022 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 337) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/337: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)[C@H]2CCCC[C@@H]21) `ZINC001472538022.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472538022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472538022 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)[C@H]2CCCC[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', 'H', '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'] dock atom type numbers: [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, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 27, 27, 4, 27, 27, 27, 27, 27, 27, 4, 4, 1, 1, 1, 2, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 27, 27, 4, 27, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: 76 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538022 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472538022 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538022/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538022/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538022 Building ZINC001472538030 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538030' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538030 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472538030 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538030/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538030 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/338 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/338' -> `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)N1C[C@H](C)[C@@H]2CCCC[C@H]21) `ZINC001472538030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472538030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472538030 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)[C@@H]2CCCC[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', 'H', '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'] dock atom type numbers: [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, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 26, 26, 4, 26, 26, 26, 26, 26, 26, 4, 4, 1, 1, 1, 2, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 26, 26, 6, 26, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: 78 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538030 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538030/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538030 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 339) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/339 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/339' -> `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)N1C[C@H](C)[C@@H]2CCCC[C@H]21) `ZINC001472538030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472538030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472538030 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)[C@@H]2CCCC[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', 'H', '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'] dock atom type numbers: [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, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 32, 32, 3, 32, 32, 32, 32, 32, 32, 3, 3, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 32, 32, 3, 32, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 84 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538030 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472538030 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538030/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538030/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538030 Building ZINC001472538030 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538030' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538030 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472538030 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538030/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538030 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 338) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/338: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)[C@@H]2CCCC[C@H]21) `ZINC001472538030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472538030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472538030 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)[C@@H]2CCCC[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', 'H', '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'] dock atom type numbers: [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, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 26, 26, 4, 26, 26, 26, 26, 26, 26, 4, 4, 1, 1, 1, 2, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 26, 26, 6, 26, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: 78 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538030 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538030/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538030 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 339) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/339: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)[C@@H]2CCCC[C@H]21) `ZINC001472538030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472538030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472538030 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)[C@@H]2CCCC[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', 'H', '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'] dock atom type numbers: [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, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 32, 32, 3, 32, 32, 32, 32, 32, 32, 3, 3, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 32, 32, 3, 32, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 84 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538030 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472538030 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538030/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538030/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538030 Building ZINC001472538035 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538035' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538035 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472538035 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538035/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538035 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/340 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/340' -> `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)N1C[C@H](C)[C@H]2CCCC[C@H]21) `ZINC001472538035.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472538035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472538035 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)[C@H]2CCCC[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', 'H', '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'] dock atom type numbers: [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, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 23, 23, 4, 23, 3, 3, 3, 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: 77 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538035 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538035/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538035 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 341) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/341 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/341' -> `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)N1C[C@H](C)[C@H]2CCCC[C@H]21) `ZINC001472538035.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472538035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472538035 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)[C@H]2CCCC[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', 'H', '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'] dock atom type numbers: [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, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 19, 19, 11, 19, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 61 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538035 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472538035 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538035/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538035/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538035 Building ZINC001472538035 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538035' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538035 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472538035 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538035/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538035 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 340) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)[C@H]2CCCC[C@H]21) `ZINC001472538035.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472538035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472538035 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)[C@H]2CCCC[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', 'H', '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'] dock atom type numbers: [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, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 23, 23, 4, 23, 3, 3, 3, 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: 77 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538035 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538035/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538035 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 341) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)[C@H]2CCCC[C@H]21) `ZINC001472538035.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472538035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472538035 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)[C@H]2CCCC[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', 'H', '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'] dock atom type numbers: [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, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 19, 19, 11, 19, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 61 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538035 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472538035 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538035/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538035/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472538035 Building ZINC001472553310 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001472553310 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/342 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/342' -> `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]1C[C@H](c2ccccc2)C1) `ZINC001472553310.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472553310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472553310 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 11, 11, 3, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 12, 12, 10, 12, 12, 10, 3, 3, 3, 11, 11, 6, 11, 3, 3, 3, 2, 10, 10, 12, 12, 10, 12, 12, 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: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 343) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/343 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/343' -> `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]1C[C@H](c2ccccc2)C1) `ZINC001472553310.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472553310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472553310 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 12, 12, 10, 12, 12, 10, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 10, 10, 12, 12, 10, 12, 12, 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: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 344) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/344 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/344' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](c2ccccc2)C1) `ZINC001472553310.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001472553310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472553310 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 15, 15, 10, 15, 15, 10, 2, 2, 2, 9, 9, 3, 9, 2, 2, 2, 3, 10, 10, 15, 15, 15, 15, 15, 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: 84 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 345) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/345 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/345' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](c2ccccc2)C1) `ZINC001472553310.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001472553310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472553310 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 15, 15, 10, 15, 15, 10, 2, 2, 2, 9, 9, 4, 9, 2, 2, 2, 3, 10, 10, 15, 15, 10, 15, 15, 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: 76 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472553310 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 Building ZINC001472553310 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001472553310 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 342) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2ccccc2)C1) `ZINC001472553310.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472553310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472553310 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 11, 11, 3, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 12, 12, 10, 12, 12, 10, 3, 3, 3, 11, 11, 6, 11, 3, 3, 3, 2, 10, 10, 12, 12, 10, 12, 12, 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: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 343) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2ccccc2)C1) `ZINC001472553310.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472553310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472553310 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 12, 12, 10, 12, 12, 10, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 10, 10, 12, 12, 10, 12, 12, 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: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 344) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/344: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](c2ccccc2)C1) `ZINC001472553310.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001472553310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472553310 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 15, 15, 10, 15, 15, 10, 2, 2, 2, 9, 9, 3, 9, 2, 2, 2, 3, 10, 10, 15, 15, 15, 15, 15, 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: 84 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 345) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/345: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](c2ccccc2)C1) `ZINC001472553310.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001472553310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472553310 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 15, 15, 10, 15, 15, 10, 2, 2, 2, 9, 9, 4, 9, 2, 2, 2, 3, 10, 10, 15, 15, 10, 15, 15, 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: 76 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472553310 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 Building ZINC001472553310 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001472553310 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 342) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2ccccc2)C1) `ZINC001472553310.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472553310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472553310 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 11, 11, 3, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 12, 12, 10, 12, 12, 10, 3, 3, 3, 11, 11, 6, 11, 3, 3, 3, 2, 10, 10, 12, 12, 10, 12, 12, 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: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 343) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2ccccc2)C1) `ZINC001472553310.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472553310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472553310 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 12, 12, 10, 12, 12, 10, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 10, 10, 12, 12, 10, 12, 12, 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: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 344) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/344: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](c2ccccc2)C1) `ZINC001472553310.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001472553310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472553310 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 15, 15, 10, 15, 15, 10, 2, 2, 2, 9, 9, 3, 9, 2, 2, 2, 3, 10, 10, 15, 15, 15, 15, 15, 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: 84 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 345) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/345: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](c2ccccc2)C1) `ZINC001472553310.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001472553310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472553310 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 15, 15, 10, 15, 15, 10, 2, 2, 2, 9, 9, 4, 9, 2, 2, 2, 3, 10, 10, 15, 15, 10, 15, 15, 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: 76 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472553310 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 Building ZINC001472553310 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001472553310 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 342) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2ccccc2)C1) `ZINC001472553310.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472553310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472553310 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 11, 11, 3, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 12, 12, 10, 12, 12, 10, 3, 3, 3, 11, 11, 6, 11, 3, 3, 3, 2, 10, 10, 12, 12, 10, 12, 12, 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: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 343) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2ccccc2)C1) `ZINC001472553310.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472553310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472553310 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 12, 12, 10, 12, 12, 10, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 10, 10, 12, 12, 10, 12, 12, 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: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 344) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/344: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](c2ccccc2)C1) `ZINC001472553310.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001472553310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472553310 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 15, 15, 10, 15, 15, 10, 2, 2, 2, 9, 9, 3, 9, 2, 2, 2, 3, 10, 10, 15, 15, 15, 15, 15, 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: 84 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 345) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/345: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](c2ccccc2)C1) `ZINC001472553310.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001472553310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472553310 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 15, 15, 10, 15, 15, 10, 2, 2, 2, 9, 9, 4, 9, 2, 2, 2, 3, 10, 10, 15, 15, 10, 15, 15, 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: 76 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472553310 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553310 Building ZINC001472553338 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553338' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553338 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472553338 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553338/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553338 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/346 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/346' -> `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]1C[C@H]1c1ccc(F)cc1) `ZINC001472553338.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472553338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472553338 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type 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, 1, 1, 1, 1, 15, 1, 1, 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, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3, 2, 9, 9, 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: 67 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553338 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553338/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553338 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 347) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/347 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/347' -> `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]1C[C@H]1c1ccc(F)cc1) `ZINC001472553338.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472553338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553338/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472553338 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type 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, 1, 1, 1, 1, 15, 1, 1, 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, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 20, 20, 4, 20, 20, 20, 20, 20, 20, 4, 4, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 12, 12, 9, 9, 12, 12, 4, 4, 4, 20, 20, 4, 20, 4, 4, 4, 3, 9, 9, 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: 86 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553338 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472553338 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553338/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553338/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553338 Building ZINC001472553338 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553338' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553338 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472553338 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553338/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553338 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 346) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/346: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccc(F)cc1) `ZINC001472553338.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472553338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472553338 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type 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, 1, 1, 1, 1, 15, 1, 1, 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, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3, 2, 9, 9, 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: 67 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553338 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553338/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553338 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 347) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/347: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccc(F)cc1) `ZINC001472553338.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472553338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553338/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472553338 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1C[C@H]1c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type 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, 1, 1, 1, 1, 15, 1, 1, 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, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 20, 20, 4, 20, 20, 20, 20, 20, 20, 4, 4, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 12, 12, 9, 9, 12, 12, 4, 4, 4, 20, 20, 4, 20, 4, 4, 4, 3, 9, 9, 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: 86 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553338 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472553338 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553338/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553338/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472553338 Building ZINC001472579477 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579477' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579477 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472579477 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579477/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579477 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/348 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/348' -> `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](CC(C)(C)C)C1) `ZINC001472579477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472579477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472579477 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](CC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 21, 21, 6, 21, 21, 21, 21, 21, 21, 3, 3, 1, 1, 1, 1, 2, 3, 7, 7, 7, 7, 7, 8, 9, 9, 9, 7, 3, 3, 3, 21, 21, 10, 21, 3, 3, 3, 7, 7, 7, 7, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 9, 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: 84 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579477 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579477/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579477 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 349) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/349 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/349' -> `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](CC(C)(C)C)C1) `ZINC001472579477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472579477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472579477 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](CC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 3, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 1, 2, 3, 6, 6, 6, 6, 6, 8, 9, 9, 9, 6, 3, 3, 3, 20, 20, 4, 20, 3, 3, 3, 6, 6, 6, 6, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 9, 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, 57, 58]) total number of confs: 73 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579477 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472579477 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579477/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579477/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579477 Building ZINC001472579477 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579477' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579477 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472579477 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579477/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579477 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 348) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](CC(C)(C)C)C1) `ZINC001472579477.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472579477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472579477 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](CC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 21, 21, 6, 21, 21, 21, 21, 21, 21, 3, 3, 1, 1, 1, 1, 2, 3, 7, 7, 7, 7, 7, 8, 9, 9, 9, 7, 3, 3, 3, 21, 21, 10, 21, 3, 3, 3, 7, 7, 7, 7, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 9, 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: 84 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579477 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579477/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579477 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 349) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](CC(C)(C)C)C1) `ZINC001472579477.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472579477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579477/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472579477 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](CC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 3, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 1, 2, 3, 6, 6, 6, 6, 6, 8, 9, 9, 9, 6, 3, 3, 3, 20, 20, 4, 20, 3, 3, 3, 6, 6, 6, 6, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 9, 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, 57, 58]) total number of confs: 73 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579477 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472579477 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579477/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579477/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579477 Building ZINC001472579478 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579478' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579478 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472579478 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579478/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579478 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/350 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/350' -> `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](CC(C)(C)C)C1) `ZINC001472579478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472579478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472579478 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 18, 18, 11, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 7, 8, 8, 8, 5, 3, 3, 3, 18, 18, 13, 18, 3, 3, 3, 5, 5, 5, 5, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 69 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579478 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579478/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579478 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 351) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/351 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/351' -> `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](CC(C)(C)C)C1) `ZINC001472579478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472579478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472579478 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](CC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 10, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 7, 8, 8, 8, 5, 3, 3, 3, 20, 20, 18, 20, 3, 3, 3, 5, 5, 5, 5, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 84 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579478 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472579478 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579478/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579478/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579478 Building ZINC001472579478 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579478' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579478 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472579478 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579478/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579478 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 350) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CC(C)(C)C)C1) `ZINC001472579478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472579478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472579478 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 18, 18, 11, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 7, 8, 8, 8, 5, 3, 3, 3, 18, 18, 13, 18, 3, 3, 3, 5, 5, 5, 5, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 69 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579478 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579478/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579478 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 351) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](CC(C)(C)C)C1) `ZINC001472579478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472579478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472579478 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](CC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [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, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 10, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 7, 8, 8, 8, 5, 3, 3, 3, 20, 20, 18, 20, 3, 3, 3, 5, 5, 5, 5, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 84 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579478 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472579478 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579478/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579478/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472579478 Building ZINC001472616351 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616351' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616351 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472616351 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616351/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616351 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/352 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H](C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C1)C1CCCC1) `ZINC001472616351.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472616351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001472616351 none CC(C)(C)OC(=O)N[C@H](C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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', 'C.ar', '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', '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, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 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, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 28, 39, 21, 14, 21, 8, 8, 8, 8, 8, 8, 5, 2, 7, 1, 1, 1, 2, 2, 1, 2, 2, 8, 21, 29, 29, 29, 29, 40, 40, 40, 40, 40, 40, 40, 40, 40, 28, 14, 14, 8, 8, 8, 8, 8, 8, 2, 2, 1, 2, 2, 8, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 199 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616351 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616351/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616351 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 353) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/353 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/353' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H](C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C1)C1CCCC1) `ZINC001472616351.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472616351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616351/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001472616351 none CC(C)(C)OC(=O)N[C@H](C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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', 'C.ar', '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', '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, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 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, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 41, 40, 30, 40, 19, 13, 19, 6, 6, 6, 6, 6, 6, 3, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 19, 29, 29, 29, 29, 41, 41, 41, 41, 41, 41, 41, 41, 41, 30, 13, 13, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [51, 25, 55, 19, 20, 21, 22, 23, 24, 52, 26, 54, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 201 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616351 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472616351 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616351/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616351/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616351 Building ZINC001472616351 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616351' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616351 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472616351 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616351/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616351 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 352) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)OC(=O)N[C@H](C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C1)C1CCCC1) `ZINC001472616351.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472616351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001472616351 none CC(C)(C)OC(=O)N[C@H](C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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', 'C.ar', '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', '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, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 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, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 28, 39, 21, 14, 21, 8, 8, 8, 8, 8, 8, 5, 2, 7, 1, 1, 1, 2, 2, 1, 2, 2, 8, 21, 29, 29, 29, 29, 40, 40, 40, 40, 40, 40, 40, 40, 40, 28, 14, 14, 8, 8, 8, 8, 8, 8, 2, 2, 1, 2, 2, 8, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 199 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616351 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616351/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616351 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 353) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)OC(=O)N[C@H](C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C1)C1CCCC1) `ZINC001472616351.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472616351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616351/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001472616351 none CC(C)(C)OC(=O)N[C@H](C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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', 'C.ar', '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', '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, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 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, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 41, 40, 30, 40, 19, 13, 19, 6, 6, 6, 6, 6, 6, 3, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 19, 29, 29, 29, 29, 41, 41, 41, 41, 41, 41, 41, 41, 41, 30, 13, 13, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [51, 25, 55, 19, 20, 21, 22, 23, 24, 52, 26, 54, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 201 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616351 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472616351 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616351/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616351/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616351 Building ZINC001472616352 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616352' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616352 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472616352 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616352/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616352 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/354 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H](C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C1)C1CCCC1) `ZINC001472616352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472616352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001472616352 none CC(C)(C)OC(=O)N[C@@H](C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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', 'C.ar', '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', '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, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 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, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 29, 37, 18, 12, 18, 6, 6, 6, 6, 6, 6, 3, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 18, 31, 31, 31, 31, 37, 37, 37, 37, 37, 37, 37, 37, 37, 29, 12, 12, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [51, 25, 55, 19, 20, 21, 22, 23, 24, 52, 26, 54, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616352 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616352/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616352 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 355) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/355 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/355' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H](C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C1)C1CCCC1) `ZINC001472616352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472616352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001472616352 none CC(C)(C)OC(=O)N[C@@H](C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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', 'C.ar', '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', '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, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 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, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 28, 38, 21, 14, 21, 7, 7, 7, 7, 7, 7, 4, 2, 6, 1, 1, 1, 3, 3, 1, 3, 3, 7, 21, 29, 29, 29, 29, 38, 38, 38, 38, 38, 38, 38, 38, 38, 28, 14, 14, 7, 7, 7, 7, 7, 7, 3, 3, 1, 3, 3, 7, 7, 29, 29, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616352 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472616352 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616352/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616352/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616352 Building ZINC001472616352 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616352' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616352 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472616352 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616352/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616352 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 354) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)OC(=O)N[C@@H](C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C1)C1CCCC1) `ZINC001472616352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472616352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001472616352 none CC(C)(C)OC(=O)N[C@@H](C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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', 'C.ar', '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', '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, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 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, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 29, 37, 18, 12, 18, 6, 6, 6, 6, 6, 6, 3, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 18, 31, 31, 31, 31, 37, 37, 37, 37, 37, 37, 37, 37, 37, 29, 12, 12, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [51, 25, 55, 19, 20, 21, 22, 23, 24, 52, 26, 54, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616352 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616352/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616352 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 355) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)OC(=O)N[C@@H](C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C1)C1CCCC1) `ZINC001472616352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472616352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001472616352 none CC(C)(C)OC(=O)N[C@@H](C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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', 'C.ar', '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', '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, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 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, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 28, 38, 21, 14, 21, 7, 7, 7, 7, 7, 7, 4, 2, 6, 1, 1, 1, 3, 3, 1, 3, 3, 7, 21, 29, 29, 29, 29, 38, 38, 38, 38, 38, 38, 38, 38, 38, 28, 14, 14, 7, 7, 7, 7, 7, 7, 3, 3, 1, 3, 3, 7, 7, 29, 29, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616352 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472616352 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616352/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616352/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616352 Building ZINC001472616353 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616353' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616353 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472616353 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616353/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616353 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/356 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H](C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C1)C1CCCC1) `ZINC001472616353.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472616353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001472616353 none CC(C)(C)OC(=O)N[C@@H](C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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', 'C.ar', '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', '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, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 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, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 41, 34, 20, 34, 15, 8, 15, 4, 4, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 17, 28, 28, 28, 28, 41, 41, 41, 41, 41, 41, 41, 41, 41, 20, 8, 8, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [51, 25, 55, 19, 20, 21, 22, 23, 24, 52, 26, 54, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 191 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616353 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616353/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616353 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 357) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/357 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/357' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H](C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C1)C1CCCC1) `ZINC001472616353.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472616353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616353/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001472616353 none CC(C)(C)OC(=O)N[C@@H](C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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', 'C.ar', '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', '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, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 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, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 25, 35, 18, 12, 18, 5, 5, 5, 5, 5, 5, 3, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 19, 31, 31, 31, 31, 42, 42, 42, 42, 42, 42, 42, 42, 42, 25, 12, 12, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [51, 25, 55, 19, 20, 21, 22, 23, 24, 52, 26, 54, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 197 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616353 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472616353 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616353/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616353/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616353 Building ZINC001472616353 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616353' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616353 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472616353 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616353/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616353 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 356) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)OC(=O)N[C@@H](C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C1)C1CCCC1) `ZINC001472616353.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472616353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001472616353 none CC(C)(C)OC(=O)N[C@@H](C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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', 'C.ar', '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', '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, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 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, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 41, 34, 20, 34, 15, 8, 15, 4, 4, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 17, 28, 28, 28, 28, 41, 41, 41, 41, 41, 41, 41, 41, 41, 20, 8, 8, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [51, 25, 55, 19, 20, 21, 22, 23, 24, 52, 26, 54, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 191 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616353 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616353/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616353 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 357) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)OC(=O)N[C@@H](C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C1)C1CCCC1) `ZINC001472616353.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472616353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616353/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001472616353 none CC(C)(C)OC(=O)N[C@@H](C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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', 'C.ar', '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', '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, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 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, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 25, 35, 18, 12, 18, 5, 5, 5, 5, 5, 5, 3, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 19, 31, 31, 31, 31, 42, 42, 42, 42, 42, 42, 42, 42, 42, 25, 12, 12, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [51, 25, 55, 19, 20, 21, 22, 23, 24, 52, 26, 54, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 197 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616353 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472616353 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616353/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616353/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616353 Building ZINC001472616354 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616354' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616354 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472616354 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616354/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616354 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/358 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H](C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C1)C1CCCC1) `ZINC001472616354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472616354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001472616354 none CC(C)(C)OC(=O)N[C@H](C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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', 'C.ar', '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', '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, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 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, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 41, 41, 30, 21, 30, 14, 8, 14, 3, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 16, 28, 28, 28, 28, 41, 41, 41, 41, 41, 41, 41, 41, 41, 21, 8, 8, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [51, 25, 55, 17, 19, 20, 21, 22, 23, 24, 52, 26, 54, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 195 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616354 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616354/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616354 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 359) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/359 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/359' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H](C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C1)C1CCCC1) `ZINC001472616354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472616354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001472616354 none CC(C)(C)OC(=O)N[C@H](C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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', 'C.ar', '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', '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, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 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, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 41, 31, 18, 31, 13, 7, 13, 3, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 3, 15, 27, 27, 27, 27, 41, 41, 41, 41, 41, 41, 41, 41, 41, 18, 7, 7, 3, 3, 3, 3, 3, 3, 2, 2, 1, 2, 2, 3, 3, 27, 27, 27, 27, 27, 27, 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, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 193 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616354 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472616354 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616354/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616354/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616354 Building ZINC001472616354 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616354' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616354 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472616354 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616354/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616354 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 358) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)OC(=O)N[C@H](C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C1)C1CCCC1) `ZINC001472616354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472616354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001472616354 none CC(C)(C)OC(=O)N[C@H](C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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', 'C.ar', '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', '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, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 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, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 41, 41, 30, 21, 30, 14, 8, 14, 3, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 16, 28, 28, 28, 28, 41, 41, 41, 41, 41, 41, 41, 41, 41, 21, 8, 8, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [51, 25, 55, 17, 19, 20, 21, 22, 23, 24, 52, 26, 54, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 195 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616354 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616354/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616354 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 359) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)OC(=O)N[C@H](C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C1)C1CCCC1) `ZINC001472616354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472616354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001472616354 none CC(C)(C)OC(=O)N[C@H](C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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', 'C.ar', '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', '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, 7, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 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, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 41, 31, 18, 31, 13, 7, 13, 3, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 3, 15, 27, 27, 27, 27, 41, 41, 41, 41, 41, 41, 41, 41, 41, 18, 7, 7, 3, 3, 3, 3, 3, 3, 2, 2, 1, 2, 2, 3, 3, 27, 27, 27, 27, 27, 27, 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, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 193 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616354 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472616354 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616354/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616354/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472616354 Building ZINC001472623078 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472623078' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472623078 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472623078 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472623078/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472623078 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/360 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnn(C2CCCC2)c1) `ZINC001472623078.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472623078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472623078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472623078 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnn(C2CCCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 5, 5, 5, 5, 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] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 7, 14, 14, 14, 14, 7, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472623078 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472623078/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472623078 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 361) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/361 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/361' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnn(C2CCCC2)c1) `ZINC001472623078.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472623078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472623078/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472623078 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnn(C2CCCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 5, 5, 5, 5, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 15, 15, 15, 15, 7, 3, 3, 3, 10, 10, 3, 10, 3, 3, 3, 2, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472623078 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472623078 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472623078/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472623078/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472623078 Building ZINC001472623078 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472623078' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472623078 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472623078 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472623078/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472623078 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 360) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnn(C2CCCC2)c1) `ZINC001472623078.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472623078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472623078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472623078 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnn(C2CCCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 5, 5, 5, 5, 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] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 7, 14, 14, 14, 14, 7, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472623078 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472623078/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472623078 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 361) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnn(C2CCCC2)c1) `ZINC001472623078.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472623078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472623078/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001472623078 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnn(C2CCCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 5, 5, 5, 5, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 15, 15, 15, 15, 7, 3, 3, 3, 10, 10, 3, 10, 3, 3, 3, 2, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472623078 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001472623078 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472623078/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472623078/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001472623078 Building ZINC001546216496 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216496' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216496 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001546216496 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216496/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216496 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/362 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN([C@@H](c3ccccc3)c3ccccc3Cl)CC2)c1) `ZINC001546216496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001546216496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001546216496 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN([C@@H](c3ccccc3)c3ccccc3Cl)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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] 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, 7, 7, 7] 0 hydrogens 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, 4, 6, 14, 14, 14, 14, 22, 22, 26, 26, 26, 26, 26, 22, 25, 25, 22, 25, 25, 25, 14, 14, 6, 6, 6, 6, 2, 6, 6, 14, 14, 14, 14, 26, 26, 26, 26, 26, 25, 25, 25, 25, 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, 54, 55]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216496 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216496/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216496 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 363) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/363 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/363' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN([C@@H](c3ccccc3)c3ccccc3Cl)CC2)c1) `ZINC001546216496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001546216496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001546216496 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN([C@@H](c3ccccc3)c3ccccc3Cl)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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] 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, 7, 7, 7] 0 hydrogens 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, 4, 7, 15, 15, 15, 15, 22, 22, 25, 25, 22, 25, 25, 22, 25, 25, 22, 25, 25, 25, 15, 15, 6, 6, 6, 6, 2, 6, 6, 15, 15, 15, 15, 25, 25, 22, 25, 25, 25, 25, 25, 25, 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, 54, 55]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216496 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001546216496 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216496/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216496/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216496 Building ZINC001546216496 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216496' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216496 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001546216496 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216496/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216496 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 362) grep: /scratch/xiaobo/12845/xbi-8058088.35/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)N2CCN([C@@H](c3ccccc3)c3ccccc3Cl)CC2)c1) `ZINC001546216496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001546216496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001546216496 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN([C@@H](c3ccccc3)c3ccccc3Cl)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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] 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, 7, 7, 7] 0 hydrogens 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, 4, 6, 14, 14, 14, 14, 22, 22, 26, 26, 26, 26, 26, 22, 25, 25, 22, 25, 25, 25, 14, 14, 6, 6, 6, 6, 2, 6, 6, 14, 14, 14, 14, 26, 26, 26, 26, 26, 25, 25, 25, 25, 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, 54, 55]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216496 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216496/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216496 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 363) grep: /scratch/xiaobo/12845/xbi-8058088.35/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)N2CCN([C@@H](c3ccccc3)c3ccccc3Cl)CC2)c1) `ZINC001546216496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001546216496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001546216496 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN([C@@H](c3ccccc3)c3ccccc3Cl)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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] 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, 7, 7, 7] 0 hydrogens 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, 4, 7, 15, 15, 15, 15, 22, 22, 25, 25, 22, 25, 25, 22, 25, 25, 22, 25, 25, 25, 15, 15, 6, 6, 6, 6, 2, 6, 6, 15, 15, 15, 15, 25, 25, 22, 25, 25, 25, 25, 25, 25, 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, 54, 55]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216496 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001546216496 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216496/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216496/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216496 Building ZINC001546216497 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216497' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216497 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001546216497 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216497/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216497 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/364 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN([C@H](c3ccccc3)c3ccccc3Cl)CC2)c1) `ZINC001546216497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001546216497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001546216497 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN([C@H](c3ccccc3)c3ccccc3Cl)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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] 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, 7, 7, 7] 0 hydrogens 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, 4, 6, 14, 14, 14, 14, 23, 23, 26, 26, 23, 26, 26, 23, 26, 26, 23, 26, 26, 26, 14, 14, 6, 6, 6, 6, 2, 6, 6, 14, 14, 14, 14, 26, 26, 23, 26, 26, 26, 26, 23, 26, 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, 54, 55]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216497 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216497/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216497 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 365) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/365 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/365' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN([C@H](c3ccccc3)c3ccccc3Cl)CC2)c1) `ZINC001546216497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001546216497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001546216497 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN([C@H](c3ccccc3)c3ccccc3Cl)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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] 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, 7, 7, 7] 0 hydrogens 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, 4, 6, 17, 17, 17, 17, 24, 24, 26, 26, 24, 26, 26, 24, 26, 26, 24, 26, 26, 26, 17, 17, 6, 6, 6, 6, 2, 6, 6, 17, 17, 17, 17, 26, 26, 24, 26, 26, 26, 26, 24, 26, 17, 17, 17, 17, 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216497 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001546216497 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216497/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216497/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216497 Building ZINC001546216497 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216497' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216497 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001546216497 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216497/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216497 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 364) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN([C@H](c3ccccc3)c3ccccc3Cl)CC2)c1) `ZINC001546216497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001546216497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001546216497 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN([C@H](c3ccccc3)c3ccccc3Cl)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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] 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, 7, 7, 7] 0 hydrogens 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, 4, 6, 14, 14, 14, 14, 23, 23, 26, 26, 23, 26, 26, 23, 26, 26, 23, 26, 26, 26, 14, 14, 6, 6, 6, 6, 2, 6, 6, 14, 14, 14, 14, 26, 26, 23, 26, 26, 26, 26, 23, 26, 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, 54, 55]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216497 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216497/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216497 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 365) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN([C@H](c3ccccc3)c3ccccc3Cl)CC2)c1) `ZINC001546216497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001546216497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001546216497 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN([C@H](c3ccccc3)c3ccccc3Cl)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 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] 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, 7, 7, 7] 0 hydrogens 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, 4, 6, 17, 17, 17, 17, 24, 24, 26, 26, 24, 26, 26, 24, 26, 26, 24, 26, 26, 26, 17, 17, 6, 6, 6, 6, 2, 6, 6, 17, 17, 17, 17, 26, 26, 24, 26, 26, 26, 26, 24, 26, 17, 17, 17, 17, 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216497 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001546216497 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216497/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216497/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001546216497 Building ZINC001514552111 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552111' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552111 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001514552111 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552111/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552111 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/366 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](Cc1ccccc1)c1ccccc1) `ZINC001514552111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001514552111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001514552111 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](Cc1ccccc1)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.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 16, 37, 35, 43, 43, 43, 43, 43, 43, 37, 37, 37, 37, 37, 37, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 3, 16, 16, 43, 43, 43, 43, 43, 43, 43, 37, 37, 37, 37, 37] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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: 222 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552111 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552111/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552111 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 367) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/367 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/367' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](Cc1ccccc1)c1ccccc1) `ZINC001514552111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001514552111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001514552111 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](Cc1ccccc1)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.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 13, 36, 35, 43, 43, 43, 43, 43, 43, 36, 36, 36, 36, 36, 36, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 2, 13, 13, 43, 43, 43, 43, 43, 43, 43, 36, 36, 36, 36, 36] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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: 219 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552111 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001514552111 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552111/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552111/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552111 Building ZINC001514552111 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552111' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552111 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001514552111 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552111/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552111 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 366) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](Cc1ccccc1)c1ccccc1) `ZINC001514552111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001514552111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001514552111 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](Cc1ccccc1)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.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 16, 37, 35, 43, 43, 43, 43, 43, 43, 37, 37, 37, 37, 37, 37, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 3, 16, 16, 43, 43, 43, 43, 43, 43, 43, 37, 37, 37, 37, 37] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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: 222 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552111 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552111/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552111 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 367) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](Cc1ccccc1)c1ccccc1) `ZINC001514552111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001514552111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001514552111 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](Cc1ccccc1)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.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 13, 36, 35, 43, 43, 43, 43, 43, 43, 36, 36, 36, 36, 36, 36, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 2, 13, 13, 43, 43, 43, 43, 43, 43, 43, 36, 36, 36, 36, 36] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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: 219 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552111 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001514552111 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552111/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552111/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552111 Building ZINC001514552116 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552116' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552116 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001514552116 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552116/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552116 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/368 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](Cc1ccccc1)c1ccccc1) `ZINC001514552116.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001514552116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001514552116 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](Cc1ccccc1)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.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 16, 37, 36, 44, 44, 44, 44, 44, 44, 37, 38, 38, 37, 38, 38, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 4, 16, 16, 44, 44, 44, 44, 44, 44, 44, 38, 38, 37, 38, 38] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552116 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552116/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552116 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 369) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/369 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/369' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](Cc1ccccc1)c1ccccc1) `ZINC001514552116.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001514552116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552116/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001514552116 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](Cc1ccccc1)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.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 15, 37, 35, 44, 44, 44, 44, 44, 44, 37, 37, 37, 37, 37, 37, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 15, 15, 44, 44, 44, 44, 44, 44, 44, 37, 37, 37, 37, 37] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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: 225 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552116 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001514552116 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552116/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552116/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552116 Building ZINC001514552116 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552116' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552116 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001514552116 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552116/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552116 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 368) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](Cc1ccccc1)c1ccccc1) `ZINC001514552116.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001514552116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001514552116 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](Cc1ccccc1)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.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 16, 37, 36, 44, 44, 44, 44, 44, 44, 37, 38, 38, 37, 38, 38, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 4, 16, 16, 44, 44, 44, 44, 44, 44, 44, 38, 38, 37, 38, 38] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552116 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552116/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552116 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 369) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](Cc1ccccc1)c1ccccc1) `ZINC001514552116.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001514552116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552116/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001514552116 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](Cc1ccccc1)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.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 15, 37, 35, 44, 44, 44, 44, 44, 44, 37, 37, 37, 37, 37, 37, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 15, 15, 44, 44, 44, 44, 44, 44, 44, 37, 37, 37, 37, 37] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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: 225 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552116 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001514552116 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552116/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552116/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514552116 Building ZINC001514652119 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514652119' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514652119 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001514652119 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514652119/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514652119 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/370 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1)C(=O)C(F)(F)F) `ZINC001514652119.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001514652119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514652119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001514652119 none CCN(Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1)C(=O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 11, 5, 15, 15, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 45, 32, 11, 11, 2, 11, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 45, 45, 45, 45, 45, 45, 47, 47, 47, 47, 47, 32, 32, 2, 11, 11, 2, 3, 1, 3, 11] 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]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514652119 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514652119/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514652119 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 371) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/371 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/371' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1)C(=O)C(F)(F)F) `ZINC001514652119.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001514652119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514652119/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001514652119 none CCN(Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1)C(=O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 11, 5, 15, 15, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 44, 31, 11, 11, 11, 11, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 44, 44, 44, 44, 44, 44, 46, 46, 46, 46, 46, 31, 31, 11, 11, 11, 2, 3, 1, 3, 11] 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]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514652119 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001514652119 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514652119/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514652119/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514652119 Building ZINC001514652119 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514652119' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514652119 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001514652119 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514652119/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514652119 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 370) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCN(Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1)C(=O)C(F)(F)F) `ZINC001514652119.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001514652119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514652119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001514652119 none CCN(Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1)C(=O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 11, 5, 15, 15, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 45, 32, 11, 11, 2, 11, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 45, 45, 45, 45, 45, 45, 47, 47, 47, 47, 47, 32, 32, 2, 11, 11, 2, 3, 1, 3, 11] 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]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514652119 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514652119/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514652119 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 371) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCN(Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1)C(=O)C(F)(F)F) `ZINC001514652119.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001514652119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514652119/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001514652119 none CCN(Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1)C(=O)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 11, 5, 15, 15, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 44, 31, 11, 11, 11, 11, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 44, 44, 44, 44, 44, 44, 46, 46, 46, 46, 46, 31, 31, 11, 11, 11, 2, 3, 1, 3, 11] 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]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514652119 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001514652119 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514652119/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514652119/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514652119 Building ZINC001514666183 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666183' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666183 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001514666183 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666183/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666183 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/372 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/372' -> `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)Nc1ccc(Cl)cc1Cl) `ZINC001514666183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001514666183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001514666183 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C(=O)Nc1ccc(Cl)cc1Cl 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', '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'] 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, 1, 16, 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, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27, 45, 45, 45, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 27, 45, 45, 45] 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: 103 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666183 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666183/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666183 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 373) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/373 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/373' -> `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)Nc1ccc(Cl)cc1Cl) `ZINC001514666183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001514666183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001514666183 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C(=O)Nc1ccc(Cl)cc1Cl 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', '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'] 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, 1, 16, 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, 29, 29, 29, 47, 47, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 29, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 109 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666183 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001514666183 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666183/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666183/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666183 Building ZINC001514666183 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666183' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666183 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001514666183 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666183/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666183 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 372) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C(=O)Nc1ccc(Cl)cc1Cl) `ZINC001514666183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001514666183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001514666183 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C(=O)Nc1ccc(Cl)cc1Cl 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', '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'] 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, 1, 16, 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, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27, 45, 45, 45, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 27, 45, 45, 45] 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: 103 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666183 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666183/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666183 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 373) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C(=O)Nc1ccc(Cl)cc1Cl) `ZINC001514666183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001514666183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001514666183 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C(=O)Nc1ccc(Cl)cc1Cl 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', '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'] 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, 1, 16, 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, 29, 29, 29, 47, 47, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 29, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 109 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666183 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001514666183 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666183/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666183/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666183 Building ZINC001514666184 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666184' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666184 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001514666184 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666184/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666184 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/374 `/scratch/xiaobo/12845/xbi-8058088.35/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)N1CCCC[C@H]1C(=O)Nc1ccc(Cl)cc1Cl) `ZINC001514666184.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001514666184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001514666184 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C(=O)Nc1ccc(Cl)cc1Cl 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', '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'] 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, 1, 16, 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, 29, 29, 29, 47, 47, 29, 45, 47, 47, 47, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 29, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 184 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666184 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666184/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666184 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 375) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/375 `/scratch/xiaobo/12845/xbi-8058088.35/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)N1CCCC[C@H]1C(=O)Nc1ccc(Cl)cc1Cl) `ZINC001514666184.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001514666184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666184/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001514666184 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C(=O)Nc1ccc(Cl)cc1Cl 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', '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'] 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, 1, 16, 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, 9, 9, 9, 9, 9, 9, 9, 28, 28, 28, 47, 47, 28, 45, 47, 47, 47, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 28, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 180 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666184 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001514666184 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666184/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666184/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666184 Building ZINC001514666184 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666184' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666184 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001514666184 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666184/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666184 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 374) grep: /scratch/xiaobo/12845/xbi-8058088.35/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)N1CCCC[C@H]1C(=O)Nc1ccc(Cl)cc1Cl) `ZINC001514666184.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001514666184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001514666184 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C(=O)Nc1ccc(Cl)cc1Cl 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', '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'] 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, 1, 16, 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, 29, 29, 29, 47, 47, 29, 45, 47, 47, 47, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 29, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 184 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666184 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666184/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666184 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 375) grep: /scratch/xiaobo/12845/xbi-8058088.35/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)N1CCCC[C@H]1C(=O)Nc1ccc(Cl)cc1Cl) `ZINC001514666184.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001514666184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666184/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001514666184 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C(=O)Nc1ccc(Cl)cc1Cl 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', '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'] 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, 1, 16, 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, 9, 9, 9, 9, 9, 9, 9, 28, 28, 28, 47, 47, 28, 45, 47, 47, 47, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 28, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 180 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666184 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001514666184 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666184/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666184/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514666184 Building ZINC001514770781 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514770781' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514770781 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001514770781 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514770781/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514770781 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/376 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(Cc2cccc(Cl)c2)s1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001514770781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001514770781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514770781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001514770781 none O=C(Nc1nnc(Cc2cccc(Cl)c2)s1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 5, 1, 1, 1, 1, 1, 16, 1, 14, 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, 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: [2, 1, 2, 2, 4, 4, 4, 4, 23, 50, 50, 50, 50, 50, 50, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 23, 23, 50, 50, 50, 50, 2, 1, 2] 50 rigid atoms, others: [1, 16, 17, 18] 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]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514770781 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514770781/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514770781 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 377) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/377 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/377' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nnc(Cc2cccc(Cl)c2)s1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001514770781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001514770781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514770781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001514770781 none O=C(Nc1nnc(Cc2cccc(Cl)c2)s1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 5, 1, 1, 1, 1, 1, 16, 1, 14, 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, 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: [2, 1, 2, 2, 4, 4, 4, 4, 23, 50, 50, 50, 50, 50, 50, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 23, 23, 50, 50, 50, 50, 2, 1, 2] 50 rigid atoms, others: [1, 16, 17, 18] 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]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514770781 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001514770781 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514770781/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514770781/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514770781 Building ZINC001514770781 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514770781' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514770781 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001514770781 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514770781/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514770781 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 376) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1nnc(Cc2cccc(Cl)c2)s1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001514770781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001514770781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514770781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001514770781 none O=C(Nc1nnc(Cc2cccc(Cl)c2)s1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 5, 1, 1, 1, 1, 1, 16, 1, 14, 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, 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: [2, 1, 2, 2, 4, 4, 4, 4, 23, 50, 50, 50, 50, 50, 50, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 23, 23, 50, 50, 50, 50, 2, 1, 2] 50 rigid atoms, others: [1, 16, 17, 18] 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]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514770781 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514770781/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514770781 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 377) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1nnc(Cc2cccc(Cl)c2)s1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001514770781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001514770781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514770781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001514770781 none O=C(Nc1nnc(Cc2cccc(Cl)c2)s1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 5, 1, 1, 1, 1, 1, 16, 1, 14, 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, 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: [2, 1, 2, 2, 4, 4, 4, 4, 23, 50, 50, 50, 50, 50, 50, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 23, 23, 50, 50, 50, 50, 2, 1, 2] 50 rigid atoms, others: [1, 16, 17, 18] 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]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514770781 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001514770781 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514770781/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514770781/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514770781 Building ZINC001514869098 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514869098' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514869098 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001514869098 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514869098/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514869098 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/378 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/378' -> `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])c2ccc3c(c2)CCC3)c1) `ZINC001514869098.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001514869098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514869098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001514869098 none CC(C)(C)OC(=O)c1ccc(Br)c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)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', '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'] 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, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 8, 16, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514869098 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514869098/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514869098 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 379) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/379 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/379' -> `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])c2ccc3c(c2)CCC3)c1) `ZINC001514869098.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001514869098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514869098/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001514869098 none CC(C)(C)OC(=O)c1ccc(Br)c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)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', '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'] 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, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 28, 28, 20, 9, 20, 9, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9, 9, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514869098 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001514869098 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514869098/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514869098/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514869098 Building ZINC001514869098 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514869098' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514869098 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001514869098 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514869098/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514869098 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 378) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)OC(=O)c1ccc(Br)c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC001514869098.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001514869098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514869098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001514869098 none CC(C)(C)OC(=O)c1ccc(Br)c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)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', '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'] 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, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 8, 16, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514869098 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514869098/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514869098 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 379) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)OC(=O)c1ccc(Br)c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC001514869098.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001514869098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514869098/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001514869098 none CC(C)(C)OC(=O)c1ccc(Br)c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)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', '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'] 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, 1, 1, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 28, 28, 20, 9, 20, 9, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9, 9, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514869098 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001514869098 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514869098/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514869098/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001514869098 Building ZINC001515017328 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017328' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017328 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515017328 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017328/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017328 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/380 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)COc1ccccc1[C@@H](CC(C)C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001515017328.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515017328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001515017328 none CC(C)COc1ccccc1[C@@H](CC(C)C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 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.ar', 'C.ar', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 29, 13, 7, 7, 7, 5, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 29, 25, 25, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 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/12845/xbi-8058088.35/working/building/ZINC001515017328 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017328/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017328 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 381) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/381 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/381' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)COc1ccccc1[C@@H](CC(C)C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001515017328.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515017328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017328/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001515017328 none CC(C)COc1ccccc1[C@@H](CC(C)C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 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.ar', 'C.ar', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 27, 13, 7, 7, 7, 5, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 23, 23, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017328 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515017328 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017328/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017328/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017328 Building ZINC001515017328 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017328' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017328 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515017328 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017328/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017328 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 380) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)COc1ccccc1[C@@H](CC(C)C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001515017328.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515017328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001515017328 none CC(C)COc1ccccc1[C@@H](CC(C)C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 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.ar', 'C.ar', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 29, 13, 7, 7, 7, 5, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 29, 25, 25, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 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/12845/xbi-8058088.35/working/building/ZINC001515017328 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017328/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017328 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 381) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)COc1ccccc1[C@@H](CC(C)C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001515017328.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515017328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017328/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001515017328 none CC(C)COc1ccccc1[C@@H](CC(C)C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 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.ar', 'C.ar', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 27, 13, 7, 7, 7, 5, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 23, 23, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017328 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515017328 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017328/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017328/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017328 Building ZINC001515017329 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017329' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017329 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515017329 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017329/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017329 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/382 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)COc1ccccc1[C@H](CC(C)C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001515017329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515017329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001515017329 none CC(C)COc1ccccc1[C@H](CC(C)C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 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.ar', 'C.ar', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 34, 15, 12, 12, 12, 9, 12, 12, 6, 4, 6, 6, 10, 10, 10, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 34, 34, 34, 34, 34, 34, 34, 27, 27, 12, 12, 12, 12, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 7, 7, 7, 7, 7, 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, 59, 60, 61, 62]) total number of confs: 206 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017329 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017329/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017329 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 383) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/383 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/383' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)COc1ccccc1[C@H](CC(C)C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001515017329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515017329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001515017329 none CC(C)COc1ccccc1[C@H](CC(C)C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 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.ar', 'C.ar', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 33, 14, 11, 11, 11, 9, 11, 11, 6, 4, 6, 6, 10, 10, 10, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 33, 33, 33, 33, 33, 33, 33, 26, 26, 11, 11, 11, 11, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 7, 7, 7, 7, 7, 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, 59, 60, 61, 62]) total number of confs: 197 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017329 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515017329 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017329/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017329/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017329 Building ZINC001515017329 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017329' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017329 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515017329 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017329/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017329 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 382) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)COc1ccccc1[C@H](CC(C)C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001515017329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515017329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001515017329 none CC(C)COc1ccccc1[C@H](CC(C)C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 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.ar', 'C.ar', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 34, 15, 12, 12, 12, 9, 12, 12, 6, 4, 6, 6, 10, 10, 10, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 34, 34, 34, 34, 34, 34, 34, 27, 27, 12, 12, 12, 12, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 7, 7, 7, 7, 7, 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, 59, 60, 61, 62]) total number of confs: 206 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017329 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017329/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017329 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 383) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)COc1ccccc1[C@H](CC(C)C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001515017329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515017329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001515017329 none CC(C)COc1ccccc1[C@H](CC(C)C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 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.ar', 'C.ar', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 33, 14, 11, 11, 11, 9, 11, 11, 6, 4, 6, 6, 10, 10, 10, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 33, 33, 33, 33, 33, 33, 33, 26, 26, 11, 11, 11, 11, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 7, 7, 7, 7, 7, 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, 59, 60, 61, 62]) total number of confs: 197 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017329 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515017329 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017329/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017329/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515017329 Building ZINC001515046130 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515046130' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515046130 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515046130 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515046130/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515046130 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/384 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC=C(c2ccc(Cl)c(Cl)c2)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001515046130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515046130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515046130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001515046130 none O=C(N1CC=C(c2ccc(Cl)c(Cl)c2)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)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', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 7, 7, 27, 27, 24, 27, 27, 27, 27, 7, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 27, 27, 27, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515046130 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515046130/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515046130 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 385) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/385 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/385' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC=C(c2ccc(Cl)c(Cl)c2)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001515046130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515046130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515046130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001515046130 none O=C(N1CC=C(c2ccc(Cl)c(Cl)c2)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)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', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 7, 7, 27, 27, 21, 27, 27, 27, 27, 7, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 27, 27, 27, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515046130 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515046130 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515046130/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515046130/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515046130 Building ZINC001515046130 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515046130' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515046130 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515046130 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515046130/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515046130 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 384) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(N1CC=C(c2ccc(Cl)c(Cl)c2)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001515046130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515046130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515046130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001515046130 none O=C(N1CC=C(c2ccc(Cl)c(Cl)c2)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)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', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 7, 7, 27, 27, 24, 27, 27, 27, 27, 7, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 27, 27, 27, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515046130 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515046130/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515046130 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 385) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(N1CC=C(c2ccc(Cl)c(Cl)c2)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001515046130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515046130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515046130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001515046130 none O=C(N1CC=C(c2ccc(Cl)c(Cl)c2)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)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', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 7, 7, 27, 27, 21, 27, 27, 27, 27, 7, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 27, 27, 27, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515046130 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515046130 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515046130/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515046130/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515046130 Building ZINC001515077000 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001515077000 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/386 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001515077000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515077000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001515077000 none O=C(NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 32, 32, 33, 33, 32, 33, 33, 33, 39, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 18, 18, 33, 33, 33, 33, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 387) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/387 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/387' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001515077000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515077000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001515077000 none O=C(NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 27, 27, 29, 29, 27, 27, 29, 29, 37, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 15, 15, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 159 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 388) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/388 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/388' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001515077000.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001515077000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001515077000 none O=C(NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 32, 32, 33, 33, 32, 33, 33, 33, 39, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 18, 18, 33, 33, 33, 33, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 389) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/389 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/389' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001515077000.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001515077000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001515077000 none O=C(NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 27, 27, 29, 29, 27, 27, 29, 29, 37, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 15, 15, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 159 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515077000 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 Building ZINC001515077000 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001515077000 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 386) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001515077000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515077000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001515077000 none O=C(NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 32, 32, 33, 33, 32, 33, 33, 33, 39, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 18, 18, 33, 33, 33, 33, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 387) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001515077000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515077000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001515077000 none O=C(NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 27, 27, 29, 29, 27, 27, 29, 29, 37, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 15, 15, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 159 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 388) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/388: 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(NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001515077000.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001515077000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001515077000 none O=C(NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 32, 32, 33, 33, 32, 33, 33, 33, 39, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 18, 18, 33, 33, 33, 33, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 389) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/389: 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(NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001515077000.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001515077000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001515077000 none O=C(NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 27, 27, 29, 29, 27, 27, 29, 29, 37, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 15, 15, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 159 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515077000 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 Building ZINC001515077000 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001515077000 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 386) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001515077000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515077000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001515077000 none O=C(NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 32, 32, 33, 33, 32, 33, 33, 33, 39, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 18, 18, 33, 33, 33, 33, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 387) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001515077000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515077000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001515077000 none O=C(NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 27, 27, 29, 29, 27, 27, 29, 29, 37, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 15, 15, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 159 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 388) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/388: 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(NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001515077000.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001515077000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001515077000 none O=C(NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 32, 32, 33, 33, 32, 33, 33, 33, 39, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 18, 18, 33, 33, 33, 33, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 389) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/389: 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(NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001515077000.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001515077000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001515077000 none O=C(NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 27, 27, 29, 29, 27, 27, 29, 29, 37, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 15, 15, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 159 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515077000 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 Building ZINC001515077000 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001515077000 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 386) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001515077000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515077000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001515077000 none O=C(NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 32, 32, 33, 33, 32, 33, 33, 33, 39, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 18, 18, 33, 33, 33, 33, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 387) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001515077000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515077000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001515077000 none O=C(NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 27, 27, 29, 29, 27, 27, 29, 29, 37, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 15, 15, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 159 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 388) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/388: 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(NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001515077000.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001515077000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001515077000 none O=C(NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 32, 32, 33, 33, 32, 33, 33, 33, 39, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 18, 18, 33, 33, 33, 33, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 389) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/389: 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(NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001515077000.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001515077000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001515077000 none O=C(NC[C@@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 27, 27, 29, 29, 27, 27, 29, 29, 37, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 15, 15, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 159 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515077000 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077000 Building ZINC001515077001 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001515077001 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/390 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001515077001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515077001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001515077001 none O=C(NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 26, 26, 28, 28, 26, 28, 28, 28, 36, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 14, 14, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 391) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/391 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/391' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001515077001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515077001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001515077001 none O=C(NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 32, 32, 33, 33, 32, 32, 33, 33, 38, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 18, 18, 33, 33, 33, 33, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 161 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 392) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/392 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/392' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001515077001.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001515077001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001515077001 none O=C(NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 26, 26, 28, 28, 26, 28, 28, 28, 36, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 14, 14, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 393) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/393 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/393' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001515077001.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001515077001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001515077001 none O=C(NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 32, 32, 33, 33, 32, 32, 33, 33, 38, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 18, 18, 33, 33, 33, 33, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 161 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515077001 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 Building ZINC001515077001 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001515077001 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 390) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001515077001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515077001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001515077001 none O=C(NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 26, 26, 28, 28, 26, 28, 28, 28, 36, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 14, 14, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 391) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001515077001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515077001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001515077001 none O=C(NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 32, 32, 33, 33, 32, 32, 33, 33, 38, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 18, 18, 33, 33, 33, 33, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 161 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 392) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/392: 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(NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001515077001.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001515077001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001515077001 none O=C(NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 26, 26, 28, 28, 26, 28, 28, 28, 36, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 14, 14, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 393) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/393: 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(NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001515077001.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001515077001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001515077001 none O=C(NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 32, 32, 33, 33, 32, 32, 33, 33, 38, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 18, 18, 33, 33, 33, 33, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 161 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515077001 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 Building ZINC001515077001 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001515077001 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 390) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001515077001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515077001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001515077001 none O=C(NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 26, 26, 28, 28, 26, 28, 28, 28, 36, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 14, 14, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 391) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001515077001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515077001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001515077001 none O=C(NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 32, 32, 33, 33, 32, 32, 33, 33, 38, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 18, 18, 33, 33, 33, 33, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 161 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 392) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/392: 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(NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001515077001.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001515077001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001515077001 none O=C(NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 26, 26, 28, 28, 26, 28, 28, 28, 36, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 14, 14, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 393) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/393: 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(NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001515077001.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001515077001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001515077001 none O=C(NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 32, 32, 33, 33, 32, 32, 33, 33, 38, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 18, 18, 33, 33, 33, 33, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 161 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515077001 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 Building ZINC001515077001 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001515077001 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 390) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001515077001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515077001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001515077001 none O=C(NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 26, 26, 28, 28, 26, 28, 28, 28, 36, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 14, 14, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 391) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001515077001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515077001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001515077001 none O=C(NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 32, 32, 33, 33, 32, 32, 33, 33, 38, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 18, 18, 33, 33, 33, 33, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 161 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 392) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/392: 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(NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001515077001.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001515077001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001515077001 none O=C(NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 26, 26, 28, 28, 26, 28, 28, 28, 36, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 14, 14, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 393) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/393: 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(NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001515077001.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001515077001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001515077001 none O=C(NC[C@H](c1ccc(Cl)cc1)N1CCc2sccc2C1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 1, 1, 1, 1, 16, 1, 1, 10, 5, 5, 1, 14, 1, 1, 1, 5, 5, 12, 1, 1, 1, 1, 15, 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, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 32, 32, 33, 33, 32, 32, 33, 33, 38, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 18, 18, 33, 33, 33, 33, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 4, 4] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 161 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515077001 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515077001 Building ZINC001515134811 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515134811' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515134811 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515134811 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515134811/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515134811 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/394 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)cc1C(=O)N1CCCC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001515134811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515134811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515134811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001515134811 none O=C(Nc1ccc(Cl)cc1C(=O)N1CCCC1)[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', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 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, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 8, 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, 14, 14, 14, 14, 14, 14, 14, 38, 38, 38, 38, 38, 38, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 4, 14, 14, 14, 38, 38, 38, 38, 38, 38, 38, 38, 4, 1, 4] 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]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515134811 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515134811/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515134811 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 395) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/395 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/395' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)cc1C(=O)N1CCCC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001515134811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515134811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515134811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001515134811 none O=C(Nc1ccc(Cl)cc1C(=O)N1CCCC1)[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', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 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, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 8, 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, 15, 15, 15, 15, 15, 15, 15, 39, 39, 40, 40, 40, 40, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 5, 15, 15, 15, 40, 40, 40, 40, 40, 40, 40, 40, 5, 1, 5] 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515134811 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515134811 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515134811/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515134811/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515134811 Building ZINC001515134811 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515134811' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515134811 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515134811 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515134811/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515134811 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 394) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(Nc1ccc(Cl)cc1C(=O)N1CCCC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001515134811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515134811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515134811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001515134811 none O=C(Nc1ccc(Cl)cc1C(=O)N1CCCC1)[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', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 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, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 8, 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, 14, 14, 14, 14, 14, 14, 14, 38, 38, 38, 38, 38, 38, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 4, 14, 14, 14, 38, 38, 38, 38, 38, 38, 38, 38, 4, 1, 4] 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]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515134811 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515134811/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515134811 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 395) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(Nc1ccc(Cl)cc1C(=O)N1CCCC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001515134811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515134811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515134811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001515134811 none O=C(Nc1ccc(Cl)cc1C(=O)N1CCCC1)[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', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 5, 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, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 8, 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, 15, 15, 15, 15, 15, 15, 15, 39, 39, 40, 40, 40, 40, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 5, 15, 15, 15, 40, 40, 40, 40, 40, 40, 40, 40, 5, 1, 5] 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515134811 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515134811 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515134811/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515134811/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515134811 Building ZINC001515174740 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515174740' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515174740 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515174740 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515174740/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515174740 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/396 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)F)cc1OC(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001515174740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515174740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515174740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001515174740 none O=C(Nc1ccc(OC(F)F)cc1OC(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', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 12, 5, 15, 15, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 3, 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: [3, 1, 3, 3, 8, 8, 8, 8, 33, 41, 41, 8, 8, 8, 11, 15, 15, 1, 1, 1, 5, 5, 5, 5, 5, 3, 8, 8, 41, 8, 15, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515174740 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515174740/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515174740 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 397) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/397 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/397' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)F)cc1OC(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001515174740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515174740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515174740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001515174740 none O=C(Nc1ccc(OC(F)F)cc1OC(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', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 12, 5, 15, 15, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 3, 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: [3, 1, 3, 3, 8, 8, 5, 8, 33, 41, 41, 8, 8, 8, 11, 15, 15, 1, 1, 1, 5, 5, 5, 5, 5, 3, 8, 8, 41, 8, 15, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515174740 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515174740 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515174740/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515174740/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515174740 Building ZINC001515174740 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515174740' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515174740 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515174740 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515174740/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515174740 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 396) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ccc(OC(F)F)cc1OC(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001515174740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515174740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515174740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001515174740 none O=C(Nc1ccc(OC(F)F)cc1OC(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', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 12, 5, 15, 15, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 3, 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: [3, 1, 3, 3, 8, 8, 8, 8, 33, 41, 41, 8, 8, 8, 11, 15, 15, 1, 1, 1, 5, 5, 5, 5, 5, 3, 8, 8, 41, 8, 15, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515174740 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515174740/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515174740 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 397) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ccc(OC(F)F)cc1OC(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001515174740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515174740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515174740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001515174740 none O=C(Nc1ccc(OC(F)F)cc1OC(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', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 12, 5, 15, 15, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 3, 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: [3, 1, 3, 3, 8, 8, 5, 8, 33, 41, 41, 8, 8, 8, 11, 15, 15, 1, 1, 1, 5, 5, 5, 5, 5, 3, 8, 8, 41, 8, 15, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515174740 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515174740 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515174740/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515174740/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515174740 Building ZINC001515205893 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205893' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205893 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515205893 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205893/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205893 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/398 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)([C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)c1ccc(F)c(F)c1)N1CCCC1) `ZINC001515205893.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515205893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001515205893 none CC(C)([C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)c1ccc(F)c(F)c1)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.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, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 15, 1, 15, 1, 10, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 7, 15, 4, 7, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 7, 14, 14, 14, 14, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 8, 8, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15] 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]) total number of confs: 85 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205893 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205893/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205893 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 399) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/399 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/399' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)([C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)c1ccc(F)c(F)c1)N1CCCC1) `ZINC001515205893.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515205893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001515205893 none CC(C)([C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)c1ccc(F)c(F)c1)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.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, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 15, 1, 15, 1, 10, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 7, 15, 4, 7, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 7, 13, 13, 13, 13, 13, 13, 13, 15, 17, 17, 17, 17, 15, 15, 15, 15, 15, 15, 4, 9, 9, 13, 13, 13, 17, 17, 17, 17, 17, 17, 17, 17] 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]) total number of confs: 88 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205893 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515205893 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205893/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205893/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205893 Building ZINC001515205893 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205893' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205893 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515205893 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205893/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205893 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 398) grep: /scratch/xiaobo/12845/xbi-8058088.35/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@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)c1ccc(F)c(F)c1)N1CCCC1) `ZINC001515205893.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515205893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001515205893 none CC(C)([C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)c1ccc(F)c(F)c1)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.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, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 15, 1, 15, 1, 10, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 7, 15, 4, 7, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 7, 14, 14, 14, 14, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 8, 8, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15] 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]) total number of confs: 85 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205893 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205893/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205893 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 399) grep: /scratch/xiaobo/12845/xbi-8058088.35/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@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)c1ccc(F)c(F)c1)N1CCCC1) `ZINC001515205893.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515205893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001515205893 none CC(C)([C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)c1ccc(F)c(F)c1)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.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, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 15, 1, 15, 1, 10, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 7, 15, 4, 7, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 7, 13, 13, 13, 13, 13, 13, 13, 15, 17, 17, 17, 17, 15, 15, 15, 15, 15, 15, 4, 9, 9, 13, 13, 13, 17, 17, 17, 17, 17, 17, 17, 17] 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]) total number of confs: 88 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205893 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515205893 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205893/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205893/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205893 Building ZINC001515205897 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205897' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205897 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515205897 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205897/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205897 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/400 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)([C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)c1ccc(F)c(F)c1)N1CCCC1) `ZINC001515205897.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515205897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001515205897 none CC(C)([C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)c1ccc(F)c(F)c1)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.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, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 15, 1, 15, 1, 10, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 14, 4, 7, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 7, 13, 13, 13, 13, 13, 13, 13, 14, 16, 16, 16, 16, 14, 14, 14, 14, 14, 14, 4, 9, 9, 13, 13, 13, 16, 16, 16, 16, 16, 16, 16, 16] 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]) total number of confs: 85 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205897 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205897/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205897 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 401) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/401 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/401' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)([C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)c1ccc(F)c(F)c1)N1CCCC1) `ZINC001515205897.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515205897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001515205897 none CC(C)([C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)c1ccc(F)c(F)c1)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.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, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 15, 1, 15, 1, 10, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 7, 15, 4, 7, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 7, 14, 14, 14, 14, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 8, 8, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15] 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]) total number of confs: 85 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205897 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515205897 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205897/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205897/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205897 Building ZINC001515205897 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205897' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205897 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515205897 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205897/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205897 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 400) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)([C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)c1ccc(F)c(F)c1)N1CCCC1) `ZINC001515205897.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515205897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001515205897 none CC(C)([C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)c1ccc(F)c(F)c1)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.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, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 15, 1, 15, 1, 10, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 14, 4, 7, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 7, 13, 13, 13, 13, 13, 13, 13, 14, 16, 16, 16, 16, 14, 14, 14, 14, 14, 14, 4, 9, 9, 13, 13, 13, 16, 16, 16, 16, 16, 16, 16, 16] 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]) total number of confs: 85 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205897 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205897/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205897 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 401) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)([C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)c1ccc(F)c(F)c1)N1CCCC1) `ZINC001515205897.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515205897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001515205897 none CC(C)([C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)c1ccc(F)c(F)c1)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.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, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 15, 1, 15, 1, 10, 5, 5, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 7, 15, 4, 7, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 7, 14, 14, 14, 14, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 8, 8, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15] 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]) total number of confs: 85 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205897 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515205897 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205897/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205897/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515205897 Building ZINC001515245307 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515245307' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515245307 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515245307 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515245307/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515245307 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/402 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Br)cc1c1nc(C2CC2)no1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001515245307.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515245307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515245307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001515245307 none O=C(Nc1ccc(Br)cc1c1nc(C2CC2)no1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 1, 5, 5, 5, 8, 12, 5, 12, 1, 1, 1, 1, 16, 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, 3, 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, 3, 3, 9, 9, 9, 9, 9, 9, 9, 38, 38, 38, 50, 50, 38, 38, 1, 1, 1, 3, 3, 1, 3, 3, 3, 3, 9, 9, 9, 50, 50, 50, 50, 50, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515245307 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515245307/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515245307 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 403) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/403 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/403' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Br)cc1c1nc(C2CC2)no1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001515245307.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515245307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515245307/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001515245307 none O=C(Nc1ccc(Br)cc1c1nc(C2CC2)no1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 1, 5, 5, 5, 8, 12, 5, 12, 1, 1, 1, 1, 16, 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, 3, 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, 10, 10, 10, 10, 10, 10, 10, 40, 40, 40, 50, 50, 40, 40, 1, 1, 1, 3, 3, 3, 3, 3, 3, 4, 10, 10, 10, 50, 50, 50, 50, 50, 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515245307 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515245307 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515245307/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515245307/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515245307 Building ZINC001515245307 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515245307' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515245307 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515245307 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515245307/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515245307 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 402) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ccc(Br)cc1c1nc(C2CC2)no1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001515245307.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515245307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515245307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001515245307 none O=C(Nc1ccc(Br)cc1c1nc(C2CC2)no1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 1, 5, 5, 5, 8, 12, 5, 12, 1, 1, 1, 1, 16, 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, 3, 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, 3, 3, 9, 9, 9, 9, 9, 9, 9, 38, 38, 38, 50, 50, 38, 38, 1, 1, 1, 3, 3, 1, 3, 3, 3, 3, 9, 9, 9, 50, 50, 50, 50, 50, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515245307 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515245307/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515245307 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 403) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ccc(Br)cc1c1nc(C2CC2)no1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001515245307.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515245307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515245307/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001515245307 none O=C(Nc1ccc(Br)cc1c1nc(C2CC2)no1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 1, 5, 5, 5, 8, 12, 5, 12, 1, 1, 1, 1, 16, 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, 3, 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, 10, 10, 10, 10, 10, 10, 10, 40, 40, 40, 50, 50, 40, 40, 1, 1, 1, 3, 3, 3, 3, 3, 3, 4, 10, 10, 10, 50, 50, 50, 50, 50, 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515245307 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515245307 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515245307/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515245307/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515245307 Building ZINC001515257153 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515257153' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515257153 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515257153 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515257153/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515257153 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/404 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(C(=O)c3ccc(CC(C)C)cc3)CC2)cc1Cl) `ZINC001515257153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515257153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515257153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001515257153 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(C(=O)c3ccc(CC(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', 'C.3', 'C.3', 'C.2', 'O.2', '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, 5, 5, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 10, 10, 14, 14, 10, 10, 28, 28, 28, 14, 14, 4, 4, 2, 2, 2, 4, 4, 4, 2, 2, 4, 4, 4, 4, 4, 14, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 14, 4, 4, 4, 4, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515257153 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515257153/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515257153 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 405) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/405 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/405' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(C(=O)c3ccc(CC(C)C)cc3)CC2)cc1Cl) `ZINC001515257153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515257153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515257153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001515257153 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(C(=O)c3ccc(CC(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', 'C.3', 'C.3', 'C.2', 'O.2', '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, 5, 5, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 8, 8, 13, 13, 10, 13, 26, 26, 26, 13, 13, 4, 4, 2, 2, 2, 4, 4, 4, 2, 2, 4, 4, 4, 4, 4, 13, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26, 13, 13, 4, 4, 4, 4, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515257153 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515257153 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515257153/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515257153/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515257153 Building ZINC001515257153 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515257153' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515257153 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515257153 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515257153/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515257153 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 404) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(C(=O)c3ccc(CC(C)C)cc3)CC2)cc1Cl) `ZINC001515257153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515257153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515257153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001515257153 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(C(=O)c3ccc(CC(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', 'C.3', 'C.3', 'C.2', 'O.2', '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, 5, 5, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 10, 10, 14, 14, 10, 10, 28, 28, 28, 14, 14, 4, 4, 2, 2, 2, 4, 4, 4, 2, 2, 4, 4, 4, 4, 4, 14, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 14, 4, 4, 4, 4, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515257153 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515257153/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515257153 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 405) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(C(=O)c3ccc(CC(C)C)cc3)CC2)cc1Cl) `ZINC001515257153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515257153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515257153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001515257153 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(C(=O)c3ccc(CC(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', 'C.3', 'C.3', 'C.2', 'O.2', '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, 5, 5, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 8, 8, 13, 13, 10, 13, 26, 26, 26, 13, 13, 4, 4, 2, 2, 2, 4, 4, 4, 2, 2, 4, 4, 4, 4, 4, 13, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26, 13, 13, 4, 4, 4, 4, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515257153 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515257153 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515257153/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515257153/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515257153 Building ZINC001515261469 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515261469' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515261469 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515261469 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515261469/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515261469 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/406 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCN(Cc1ccccc1)Cc1ccccc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001515261469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515261469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515261469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001515261469 none O=C(NCCCN(Cc1ccccc1)Cc1ccccc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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', 'C.ar', 'C.ar', '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', '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: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 14, 19, 22, 23, 37, 37, 23, 37, 37, 22, 23, 37, 37, 23, 37, 37, 1, 1, 1, 6, 6, 6, 6, 6, 2, 13, 13, 19, 19, 19, 19, 23, 23, 37, 37, 23, 37, 37, 23, 23, 37, 37, 23, 37, 37, 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]) total number of confs: 276 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515261469 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515261469/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515261469 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 407) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/407 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/407' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCN(Cc1ccccc1)Cc1ccccc1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001515261469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515261469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515261469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001515261469 none O=C(NCCCN(Cc1ccccc1)Cc1ccccc1)[C@]([O-])([SiH3])c1ccc(Cl)s1 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', 'C.ar', 'C.ar', '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', '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: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 19, 23, 24, 36, 36, 24, 36, 36, 23, 25, 37, 37, 25, 37, 37, 1, 1, 1, 6, 6, 6, 6, 6, 2, 14, 14, 19, 19, 19, 19, 24, 24, 36, 36, 24, 36, 36, 25, 25, 37, 37, 25, 37, 37, 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]) total number of confs: 272 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515261469 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515261469 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515261469/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515261469/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515261469 Building ZINC001515261469 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515261469' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515261469 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515261469 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515261469/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515261469 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 406) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NCCCN(Cc1ccccc1)Cc1ccccc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001515261469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515261469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515261469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001515261469 none O=C(NCCCN(Cc1ccccc1)Cc1ccccc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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', 'C.ar', 'C.ar', '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', '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: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 14, 19, 22, 23, 37, 37, 23, 37, 37, 22, 23, 37, 37, 23, 37, 37, 1, 1, 1, 6, 6, 6, 6, 6, 2, 13, 13, 19, 19, 19, 19, 23, 23, 37, 37, 23, 37, 37, 23, 23, 37, 37, 23, 37, 37, 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]) total number of confs: 276 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515261469 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515261469/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515261469 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 407) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NCCCN(Cc1ccccc1)Cc1ccccc1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001515261469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515261469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515261469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001515261469 none O=C(NCCCN(Cc1ccccc1)Cc1ccccc1)[C@]([O-])([SiH3])c1ccc(Cl)s1 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', 'C.ar', 'C.ar', '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', '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: [11, 1, 8, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 13, 19, 23, 24, 36, 36, 24, 36, 36, 23, 25, 37, 37, 25, 37, 37, 1, 1, 1, 6, 6, 6, 6, 6, 2, 14, 14, 19, 19, 19, 19, 24, 24, 36, 36, 24, 36, 36, 25, 25, 37, 37, 25, 37, 37, 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]) total number of confs: 272 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515261469 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515261469 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515261469/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515261469/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515261469 Building ZINC001515328497 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515328497' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515328497 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515328497 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515328497/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515328497 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/408 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(c2nc3ccccc3s2)o1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001515328497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515328497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515328497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001515328497 none O=C(NCc1ccc(c2nc3ccccc3s2)o1)[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', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'O.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, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 12, 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, 3, 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, 43, 43, 43, 43, 44, 44, 44, 44, 44, 44, 44, 44, 43, 1, 1, 1, 3, 3, 3, 3, 3, 2, 10, 10, 43, 43, 44, 44, 44, 44, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515328497 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515328497/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515328497 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 409) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/409 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/409' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(c2nc3ccccc3s2)o1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001515328497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515328497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515328497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001515328497 none O=C(NCc1ccc(c2nc3ccccc3s2)o1)[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', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'O.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, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 12, 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, 3, 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, 43, 43, 43, 43, 44, 44, 44, 44, 44, 44, 44, 44, 43, 1, 1, 1, 3, 3, 3, 3, 3, 2, 10, 10, 43, 43, 44, 44, 44, 44, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515328497 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515328497 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515328497/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515328497/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515328497 Building ZINC001515328497 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515328497' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515328497 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515328497 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515328497/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515328497 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 408) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NCc1ccc(c2nc3ccccc3s2)o1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001515328497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515328497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515328497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001515328497 none O=C(NCc1ccc(c2nc3ccccc3s2)o1)[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', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'O.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, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 12, 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, 3, 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, 43, 43, 43, 43, 44, 44, 44, 44, 44, 44, 44, 44, 43, 1, 1, 1, 3, 3, 3, 3, 3, 2, 10, 10, 43, 43, 44, 44, 44, 44, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515328497 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515328497/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515328497 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 409) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NCc1ccc(c2nc3ccccc3s2)o1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001515328497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515328497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515328497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001515328497 none O=C(NCc1ccc(c2nc3ccccc3s2)o1)[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', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'O.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, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 12, 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, 3, 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, 43, 43, 43, 43, 44, 44, 44, 44, 44, 44, 44, 44, 43, 1, 1, 1, 3, 3, 3, 3, 3, 2, 10, 10, 43, 43, 44, 44, 44, 44, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515328497 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515328497 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515328497/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515328497/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515328497 Building ZINC001515376045 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376045' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376045 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515376045 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376045/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376045 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/410 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](c2cccc(C(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001515376045.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515376045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001515376045 none O=C(N1CC[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', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 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, 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: [2, 1, 4, 11, 11, 11, 11, 11, 35, 35, 11, 35, 35, 35, 35, 35, 35, 11, 1, 1, 1, 4, 4, 4, 4, 4, 11, 11, 11, 11, 35, 35, 11, 35, 11, 11, 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]) total number of confs: 90 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376045 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376045/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376045 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 411) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/411 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/411' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](c2cccc(C(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001515376045.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515376045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376045/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001515376045 none O=C(N1CC[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', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 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, 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: [2, 1, 4, 11, 11, 11, 11, 11, 36, 36, 11, 36, 36, 36, 36, 36, 36, 11, 1, 1, 1, 4, 4, 4, 4, 4, 11, 11, 11, 11, 36, 36, 11, 36, 11, 11, 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376045 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515376045 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376045/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376045/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376045 Building ZINC001515376045 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376045' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376045 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515376045 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376045/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376045 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 410) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CC[C@@H](c2cccc(C(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001515376045.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515376045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001515376045 none O=C(N1CC[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', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 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, 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: [2, 1, 4, 11, 11, 11, 11, 11, 35, 35, 11, 35, 35, 35, 35, 35, 35, 11, 1, 1, 1, 4, 4, 4, 4, 4, 11, 11, 11, 11, 35, 35, 11, 35, 11, 11, 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]) total number of confs: 90 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376045 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376045/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376045 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 411) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CC[C@@H](c2cccc(C(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001515376045.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515376045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376045/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001515376045 none O=C(N1CC[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', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 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, 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: [2, 1, 4, 11, 11, 11, 11, 11, 36, 36, 11, 36, 36, 36, 36, 36, 36, 11, 1, 1, 1, 4, 4, 4, 4, 4, 11, 11, 11, 11, 36, 36, 11, 36, 11, 11, 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]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376045 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515376045 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376045/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376045/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376045 Building ZINC001515376047 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376047' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376047 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515376047 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376047/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376047 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/412 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](c2cccc(C(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001515376047.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515376047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001515376047 none O=C(N1CC[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', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 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, 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: [2, 1, 4, 11, 11, 11, 11, 11, 36, 36, 18, 36, 36, 36, 36, 36, 36, 11, 1, 1, 1, 4, 4, 4, 4, 4, 11, 11, 11, 11, 36, 36, 20, 36, 11, 11, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376047 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376047/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376047 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 413) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/413 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/413' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](c2cccc(C(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001515376047.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515376047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376047/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001515376047 none O=C(N1CC[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', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 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, 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: [2, 1, 3, 7, 7, 7, 7, 7, 34, 34, 9, 34, 34, 34, 34, 34, 34, 7, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 7, 7, 34, 34, 16, 34, 7, 7, 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]) total number of confs: 99 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376047 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515376047 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376047/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376047/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376047 Building ZINC001515376047 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376047' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376047 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515376047 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376047/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376047 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 412) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CC[C@H](c2cccc(C(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001515376047.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515376047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001515376047 none O=C(N1CC[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', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 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, 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: [2, 1, 4, 11, 11, 11, 11, 11, 36, 36, 18, 36, 36, 36, 36, 36, 36, 11, 1, 1, 1, 4, 4, 4, 4, 4, 11, 11, 11, 11, 36, 36, 20, 36, 11, 11, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376047 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376047/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376047 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 413) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CC[C@H](c2cccc(C(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001515376047.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515376047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376047/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001515376047 none O=C(N1CC[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', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 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, 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: [2, 1, 3, 7, 7, 7, 7, 7, 34, 34, 9, 34, 34, 34, 34, 34, 34, 7, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 7, 7, 34, 34, 16, 34, 7, 7, 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]) total number of confs: 99 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376047 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515376047 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376047/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376047/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515376047 Building ZINC001515466198 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515466198' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515466198 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515466198 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515466198/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515466198 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/414 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2cc(Cl)cc(Cl)c2C1) `ZINC001515466198.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515466198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515466198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001515466198 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2cc(Cl)cc(Cl)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 1, 16, 1, 1, 16, 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, 7, 12, 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: 66 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515466198 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515466198/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515466198 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 415) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/415 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/415' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2cc(Cl)cc(Cl)c2C1) `ZINC001515466198.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515466198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515466198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001515466198 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2cc(Cl)cc(Cl)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 1, 16, 1, 1, 16, 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, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 18] 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: 62 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515466198 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515466198 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515466198/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515466198/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515466198 Building ZINC001515466198 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515466198' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515466198 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515466198 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515466198/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515466198 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 414) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/414: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2cc(Cl)cc(Cl)c2C1) `ZINC001515466198.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515466198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515466198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001515466198 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2cc(Cl)cc(Cl)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 1, 16, 1, 1, 16, 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, 7, 12, 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: 66 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515466198 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515466198/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515466198 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 415) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/415: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2cc(Cl)cc(Cl)c2C1) `ZINC001515466198.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515466198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515466198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001515466198 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2cc(Cl)cc(Cl)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 1, 16, 1, 1, 16, 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, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 18] 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: 62 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515466198 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515466198 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515466198/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515466198/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515466198 Building ZINC001515502144 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515502144' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515502144 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515502144 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515502144/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515502144 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/416 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CCCC2) `ZINC001515502144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515502144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515502144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001515502144 none CC(C)(C)OC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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', 'S.3', 'C.2', 'C.2', '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, 5, 5, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 1, 1, 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, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 29, 10, 29, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 8, 5, 10, 10, 10, 10, 10, 10, 37, 37, 37, 37, 37, 37, 37, 37, 37, 2, 4, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515502144 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515502144/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515502144 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 417) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/417 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/417' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CCCC2) `ZINC001515502144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515502144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515502144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001515502144 none CC(C)(C)OC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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', 'S.3', 'C.2', 'C.2', '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, 5, 5, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 1, 1, 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, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 34, 35, 35, 25, 10, 25, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 7, 7, 4, 7, 7, 7, 5, 10, 10, 10, 10, 10, 10, 35, 35, 35, 35, 35, 35, 35, 35, 35, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515502144 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515502144 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515502144/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515502144/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515502144 Building ZINC001515502144 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515502144' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515502144 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515502144 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515502144/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515502144 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 416) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)OC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CCCC2) `ZINC001515502144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515502144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515502144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001515502144 none CC(C)(C)OC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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', 'S.3', 'C.2', 'C.2', '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, 5, 5, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 1, 1, 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, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 29, 10, 29, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 8, 5, 10, 10, 10, 10, 10, 10, 37, 37, 37, 37, 37, 37, 37, 37, 37, 2, 4, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515502144 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515502144/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515502144 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 417) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)OC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CCCC2) `ZINC001515502144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515502144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515502144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001515502144 none CC(C)(C)OC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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', 'S.3', 'C.2', 'C.2', '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, 5, 5, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 1, 1, 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, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 34, 35, 35, 25, 10, 25, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 7, 7, 4, 7, 7, 7, 5, 10, 10, 10, 10, 10, 10, 35, 35, 35, 35, 35, 35, 35, 35, 35, 2, 4, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515502144 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515502144 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515502144/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515502144/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515502144 Building ZINC001515613404 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515613404' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515613404 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515613404 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515613404/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515613404 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/418 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3cccc(C)c3)n(c3ccc(C)cc3)n2)c1) `ZINC001515613404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515613404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515613404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001515613404 none COc1cccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3cccc(C)c3)n(c3ccc(C)cc3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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.3', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 26, 7, 7, 7, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 26, 28, 28, 28, 26, 26, 26, 7, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 26] 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: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515613404 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515613404/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515613404 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 419) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/419 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/419' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3cccc(C)c3)n(c3ccc(C)cc3)n2)c1) `ZINC001515613404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515613404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515613404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001515613404 none COc1cccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3cccc(C)c3)n(c3ccc(C)cc3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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.3', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 27, 7, 7, 7, 4, 3, 1, 3, 1, 1, 1, 4, 4, 2, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 27, 28, 28, 28, 27, 27, 27, 7, 4, 4, 4, 2, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 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: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515613404 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515613404 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515613404/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515613404/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515613404 Building ZINC001515613404 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515613404' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515613404 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515613404 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515613404/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515613404 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 418) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1cccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3cccc(C)c3)n(c3ccc(C)cc3)n2)c1) `ZINC001515613404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515613404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515613404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001515613404 none COc1cccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3cccc(C)c3)n(c3ccc(C)cc3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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.3', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 26, 7, 7, 7, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 26, 28, 28, 28, 26, 26, 26, 7, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 26] 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: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515613404 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515613404/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515613404 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 419) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1cccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3cccc(C)c3)n(c3ccc(C)cc3)n2)c1) `ZINC001515613404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515613404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515613404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001515613404 none COc1cccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3cccc(C)c3)n(c3ccc(C)cc3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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.3', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 27, 27, 27, 27, 7, 7, 7, 4, 3, 1, 3, 1, 1, 1, 4, 4, 2, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 27, 28, 28, 28, 27, 27, 27, 7, 4, 4, 4, 2, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 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: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515613404 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515613404 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515613404/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515613404/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515613404 Building ZINC001515614702 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515614702' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515614702 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515614702 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515614702/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515614702 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/420 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)n(c3cccc(C)c3)n2)cc1) `ZINC001515614702.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515614702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515614702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001515614702 none COc1ccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)n(c3cccc(C)c3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 1, 1, 1, 1, 1, 5, 1, 8, 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] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 28, 28, 12, 12, 12, 7, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 12, 12, 21, 21, 21, 21, 21, 21, 12, 28, 28, 28, 28, 28, 28, 28, 12, 7, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 21, 21, 21, 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, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 124 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515614702 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515614702/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515614702 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 421) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/421 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/421' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)n(c3cccc(C)c3)n2)cc1) `ZINC001515614702.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515614702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515614702/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001515614702 none COc1ccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)n(c3cccc(C)c3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 1, 1, 1, 1, 1, 5, 1, 8, 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] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 6, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 11, 11, 21, 21, 20, 21, 21, 21, 11, 27, 27, 27, 27, 27, 27, 27, 11, 6, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 21, 21, 21, 27, 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, 49, 50, 51, 52, 53, 54]) total number of confs: 82 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515614702 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515614702 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515614702/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515614702/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515614702 Building ZINC001515614702 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515614702' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515614702 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515614702 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515614702/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515614702 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 420) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/420: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)n(c3cccc(C)c3)n2)cc1) `ZINC001515614702.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515614702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515614702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001515614702 none COc1ccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc(C)cc3)n(c3cccc(C)c3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 1, 1, 1, 1, 1, 5, 1, 8, 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] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 28, 28, 12, 12, 12, 7, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 12, 12, 21, 21, 21, 21, 21, 21, 12, 28, 28, 28, 28, 28, 28, 28, 12, 7, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 21, 21, 21, 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, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 124 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515614702 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515614702/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515614702 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 421) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/421: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)n(c3cccc(C)c3)n2)cc1) `ZINC001515614702.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515614702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515614702/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001515614702 none COc1ccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc(C)cc3)n(c3cccc(C)c3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 8, 1, 1, 1, 1, 1, 5, 1, 8, 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] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 6, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 11, 11, 21, 21, 20, 21, 21, 21, 11, 27, 27, 27, 27, 27, 27, 27, 11, 6, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 21, 21, 21, 27, 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, 49, 50, 51, 52, 53, 54]) total number of confs: 82 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515614702 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515614702 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515614702/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515614702/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515614702 Building ZINC001515683147 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515683147' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515683147 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515683147 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515683147/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515683147 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/422 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(CC)CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c2ccc(Br)cc21) `ZINC001515683147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515683147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515683147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001515683147 none CCC1(CC)CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c2ccc(Br)cc21 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', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 18, 10, 5, 2, 6, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 10, 10, 10, 10, 10, 10, 10, 17, 17, 17, 17, 17, 18, 18, 18, 18, 18, 10, 10, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 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: 148 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515683147 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515683147/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515683147 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 423) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/423 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/423' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(CC)CN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c2ccc(Br)cc21) `ZINC001515683147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515683147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515683147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001515683147 none CCC1(CC)CN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c2ccc(Br)cc21 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', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 12, 5, 2, 6, 1, 1, 1, 5, 5, 5, 5, 14, 14, 14, 5, 12, 12, 12, 12, 12, 12, 12, 20, 20, 20, 20, 20, 19, 19, 19, 19, 19, 12, 12, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 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: 155 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515683147 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515683147 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515683147/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515683147/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515683147 Building ZINC001515683147 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515683147' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515683147 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515683147 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515683147/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515683147 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 422) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCC1(CC)CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c2ccc(Br)cc21) `ZINC001515683147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515683147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515683147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001515683147 none CCC1(CC)CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c2ccc(Br)cc21 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', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 18, 10, 5, 2, 6, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 10, 10, 10, 10, 10, 10, 10, 17, 17, 17, 17, 17, 18, 18, 18, 18, 18, 10, 10, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 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: 148 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515683147 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515683147/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515683147 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 423) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCC1(CC)CN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c2ccc(Br)cc21) `ZINC001515683147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515683147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515683147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001515683147 none CCC1(CC)CN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c2ccc(Br)cc21 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', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 12, 5, 2, 6, 1, 1, 1, 5, 5, 5, 5, 14, 14, 14, 5, 12, 12, 12, 12, 12, 12, 12, 20, 20, 20, 20, 20, 19, 19, 19, 19, 19, 12, 12, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 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: 155 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515683147 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515683147 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515683147/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515683147/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515683147 Building ZINC001515705160 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515705160' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515705160 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515705160 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515705160/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515705160 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/424 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ncc(Cc2ccc(Br)c(C)c2)s1) `ZINC001515705160.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515705160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515705160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001515705160 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ncc(Cc2ccc(Br)c(C)c2)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', '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, 8, 1, 1, 5, 1, 1, 1, 1, 17, 1, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 4, 23, 50, 50, 46, 46, 50, 50, 50, 4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 23, 23, 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]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515705160 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515705160/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515705160 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 425) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/425 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/425' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ncc(Cc2ccc(Br)c(C)c2)s1) `ZINC001515705160.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515705160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515705160/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001515705160 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ncc(Cc2ccc(Br)c(C)c2)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', '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, 8, 1, 1, 5, 1, 1, 1, 1, 17, 1, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 4, 23, 50, 50, 46, 50, 50, 50, 50, 4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 23, 23, 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]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515705160 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515705160 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515705160/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515705160/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515705160 Building ZINC001515705160 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515705160' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515705160 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515705160 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515705160/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515705160 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 424) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ncc(Cc2ccc(Br)c(C)c2)s1) `ZINC001515705160.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515705160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515705160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001515705160 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ncc(Cc2ccc(Br)c(C)c2)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', '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, 8, 1, 1, 5, 1, 1, 1, 1, 17, 1, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 4, 23, 50, 50, 46, 46, 50, 50, 50, 4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 23, 23, 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]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515705160 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515705160/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515705160 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 425) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ncc(Cc2ccc(Br)c(C)c2)s1) `ZINC001515705160.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515705160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515705160/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001515705160 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ncc(Cc2ccc(Br)c(C)c2)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', '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, 8, 1, 1, 5, 1, 1, 1, 1, 17, 1, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 4, 23, 50, 50, 46, 50, 50, 50, 50, 4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 23, 23, 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]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515705160 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515705160 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515705160/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515705160/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515705160 Building ZINC001515865155 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515865155' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515865155 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515865155 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515865155/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515865155 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/426 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1)c1ccccc1) `ZINC001515865155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515865155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515865155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001515865155 none O=C(Nc1cccc(NC(=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', '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', '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, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 6, 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] 0 hydrogens 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, 14, 14, 14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 14, 26, 35, 35, 26, 35, 35, 26, 14, 14, 14, 4, 7, 7, 14, 35, 35, 26, 35, 35] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515865155 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515865155/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515865155 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 427) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/427 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/427' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1)c1ccccc1) `ZINC001515865155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515865155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515865155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001515865155 none O=C(Nc1cccc(NC(=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', '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', '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, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 6, 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] 0 hydrogens 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, 25, 14, 14, 14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 14, 25, 36, 36, 25, 36, 36, 26, 14, 14, 14, 4, 6, 6, 14, 36, 36, 25, 36, 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515865155 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515865155 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515865155/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515865155/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515865155 Building ZINC001515865155 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515865155' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515865155 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515865155 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515865155/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515865155 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 426) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1)c1ccccc1) `ZINC001515865155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515865155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515865155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001515865155 none O=C(Nc1cccc(NC(=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', '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', '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, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 6, 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] 0 hydrogens 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, 14, 14, 14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 14, 26, 35, 35, 26, 35, 35, 26, 14, 14, 14, 4, 7, 7, 14, 35, 35, 26, 35, 35] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515865155 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515865155/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515865155 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 427) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1)c1ccccc1) `ZINC001515865155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515865155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515865155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001515865155 none O=C(Nc1cccc(NC(=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', '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', '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, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 6, 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] 0 hydrogens 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, 25, 14, 14, 14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 14, 25, 36, 36, 25, 36, 36, 26, 14, 14, 14, 4, 6, 6, 14, 36, 36, 25, 36, 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515865155 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515865155 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515865155/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515865155/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515865155 Building ZINC001515886112 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886112' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886112 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515886112 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886112/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886112 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/428 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](Cn1cnc2ccccc21)c1ccc(F)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001515886112.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515886112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001515886112 none O=C(N[C@@H](Cn1cnc2ccccc21)c1ccc(F)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.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, 5, 7, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 13, 29, 29, 29, 29, 29, 29, 29, 29, 7, 9, 9, 9, 9, 9, 9, 1, 1, 1, 8, 8, 8, 8, 8, 4, 13, 13, 29, 29, 29, 29, 29, 9, 9, 9, 9, 8, 8] 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]) total number of confs: 94 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886112 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886112/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886112 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 429) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/429 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/429' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](Cn1cnc2ccccc21)c1ccc(F)cc1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001515886112.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515886112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001515886112 none O=C(N[C@@H](Cn1cnc2ccccc21)c1ccc(F)cc1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.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, 5, 7, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 14, 29, 29, 29, 29, 29, 29, 29, 29, 7, 9, 9, 9, 9, 9, 9, 1, 1, 1, 9, 9, 9, 9, 9, 4, 14, 14, 29, 29, 29, 29, 29, 9, 9, 9, 9, 9, 9] 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]) total number of confs: 97 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886112 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515886112 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886112/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886112/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886112 Building ZINC001515886112 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886112' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886112 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515886112 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886112/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886112 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 428) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N[C@@H](Cn1cnc2ccccc21)c1ccc(F)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001515886112.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515886112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001515886112 none O=C(N[C@@H](Cn1cnc2ccccc21)c1ccc(F)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.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, 5, 7, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 13, 29, 29, 29, 29, 29, 29, 29, 29, 7, 9, 9, 9, 9, 9, 9, 1, 1, 1, 8, 8, 8, 8, 8, 4, 13, 13, 29, 29, 29, 29, 29, 9, 9, 9, 9, 8, 8] 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]) total number of confs: 94 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886112 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886112/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886112 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 429) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N[C@@H](Cn1cnc2ccccc21)c1ccc(F)cc1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001515886112.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515886112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001515886112 none O=C(N[C@@H](Cn1cnc2ccccc21)c1ccc(F)cc1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.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, 5, 7, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 14, 29, 29, 29, 29, 29, 29, 29, 29, 7, 9, 9, 9, 9, 9, 9, 1, 1, 1, 9, 9, 9, 9, 9, 4, 14, 14, 29, 29, 29, 29, 29, 9, 9, 9, 9, 9, 9] 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]) total number of confs: 97 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886112 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515886112 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886112/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886112/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886112 Building ZINC001515886113 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886113' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886113 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515886113 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886113/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886113 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/430 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](Cn1cnc2ccccc21)c1ccc(F)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001515886113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515886113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001515886113 none O=C(N[C@H](Cn1cnc2ccccc21)c1ccc(F)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.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, 5, 7, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 14, 28, 28, 28, 28, 28, 28, 28, 28, 7, 9, 9, 7, 7, 9, 9, 1, 1, 1, 9, 9, 9, 9, 9, 4, 14, 14, 28, 28, 28, 28, 28, 9, 9, 9, 9, 9, 9] 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]) total number of confs: 101 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886113 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886113/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886113 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 431) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/431 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/431' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](Cn1cnc2ccccc21)c1ccc(F)cc1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001515886113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515886113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001515886113 none O=C(N[C@H](Cn1cnc2ccccc21)c1ccc(F)cc1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.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, 5, 7, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 13, 29, 29, 29, 29, 29, 29, 29, 29, 7, 9, 9, 7, 7, 9, 9, 1, 1, 1, 8, 8, 8, 8, 8, 4, 13, 13, 29, 29, 29, 29, 29, 9, 9, 9, 9, 8, 8] 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]) total number of confs: 100 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886113 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515886113 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886113/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886113/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886113 Building ZINC001515886113 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886113' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886113 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515886113 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886113/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886113 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 430) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(N[C@H](Cn1cnc2ccccc21)c1ccc(F)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001515886113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515886113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001515886113 none O=C(N[C@H](Cn1cnc2ccccc21)c1ccc(F)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.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, 5, 7, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 14, 28, 28, 28, 28, 28, 28, 28, 28, 7, 9, 9, 7, 7, 9, 9, 1, 1, 1, 9, 9, 9, 9, 9, 4, 14, 14, 28, 28, 28, 28, 28, 9, 9, 9, 9, 9, 9] 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]) total number of confs: 101 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886113 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886113/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886113 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 431) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(N[C@H](Cn1cnc2ccccc21)c1ccc(F)cc1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001515886113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515886113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001515886113 none O=C(N[C@H](Cn1cnc2ccccc21)c1ccc(F)cc1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.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, 5, 7, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 13, 29, 29, 29, 29, 29, 29, 29, 29, 7, 9, 9, 7, 7, 9, 9, 1, 1, 1, 8, 8, 8, 8, 8, 4, 13, 13, 29, 29, 29, 29, 29, 9, 9, 9, 9, 8, 8] 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]) total number of confs: 100 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886113 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515886113 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886113/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886113/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515886113 Building ZINC001515902657 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902657' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902657 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515902657 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902657/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902657 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/432 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/432' -> `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])c3cc(Cl)cc(Cl)c3)cc2F)C[C@H](C)O1) `ZINC001515902657.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515902657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001515902657 none C[C@H]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2F)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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 10, 10, 10, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 10, 10, 2, 3, 1, 3, 10, 47, 47, 47, 47, 47] 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: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902657 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902657/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902657 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 433) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/433 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/433' -> `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])c3cc(Cl)cc(Cl)c3)cc2F)C[C@H](C)O1) `ZINC001515902657.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515902657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902657/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001515902657 none C[C@H]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2F)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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 10, 10, 10, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 10, 10, 2, 3, 1, 3, 10, 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, 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/12845/xbi-8058088.35/working/building/ZINC001515902657 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515902657 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902657/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902657/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902657 Building ZINC001515902657 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902657' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902657 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515902657 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902657/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902657 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 432) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@H]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2F)C[C@H](C)O1) `ZINC001515902657.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515902657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001515902657 none C[C@H]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2F)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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 10, 10, 10, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 10, 10, 2, 3, 1, 3, 10, 47, 47, 47, 47, 47] 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: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902657 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902657/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902657 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 433) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@H]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2F)C[C@H](C)O1) `ZINC001515902657.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515902657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902657/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001515902657 none C[C@H]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2F)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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 10, 10, 10, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 10, 10, 2, 3, 1, 3, 10, 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, 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/12845/xbi-8058088.35/working/building/ZINC001515902657 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515902657 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902657/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902657/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902657 Building ZINC001515902659 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902659' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902659 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515902659 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902659/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902659 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/434 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/434' -> `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])c3cc(Cl)cc(Cl)c3)cc2F)C[C@H](C)O1) `ZINC001515902659.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515902659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001515902659 none C[C@@H]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2F)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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 13, 13, 13, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 13, 13, 13, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 13, 13, 2, 3, 1, 3, 13, 42, 42, 42, 42, 42] 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: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902659 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902659/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902659 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 435) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/435 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/435' -> `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])c3cc(Cl)cc(Cl)c3)cc2F)C[C@H](C)O1) `ZINC001515902659.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515902659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001515902659 none C[C@@H]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2F)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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 43, 43, 19, 14, 14, 14, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 14, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 14, 14, 2, 3, 1, 3, 14, 43, 43, 43, 43, 43] 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: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902659 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515902659 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902659/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902659/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902659 Building ZINC001515902659 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902659' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902659 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515902659 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902659/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902659 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 434) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@@H]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2F)C[C@H](C)O1) `ZINC001515902659.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515902659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001515902659 none C[C@@H]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2F)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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 13, 13, 13, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 13, 13, 13, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 13, 13, 2, 3, 1, 3, 13, 42, 42, 42, 42, 42] 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: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902659 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902659/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902659 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 435) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@@H]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2F)C[C@H](C)O1) `ZINC001515902659.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515902659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001515902659 none C[C@@H]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2F)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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 43, 43, 19, 14, 14, 14, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 14, 14, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 14, 14, 2, 3, 1, 3, 14, 43, 43, 43, 43, 43] 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: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902659 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515902659 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902659/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902659/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902659 Building ZINC001515902660 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902660' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902660 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515902660 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902660/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902660 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/436 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/436' -> `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])c3cc(Cl)cc(Cl)c3)cc2F)C[C@@H](C)O1) `ZINC001515902660.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515902660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001515902660 none C[C@@H]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2F)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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 10, 10, 10, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 10, 10, 2, 3, 1, 3, 10, 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, 46]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902660 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902660/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902660 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 437) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/437 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/437' -> `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])c3cc(Cl)cc(Cl)c3)cc2F)C[C@@H](C)O1) `ZINC001515902660.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515902660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902660/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001515902660 none C[C@@H]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2F)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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 10, 10, 10, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 10, 10, 2, 3, 1, 3, 10, 47, 47, 47, 47, 47] 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: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902660 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515902660 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902660/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902660/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902660 Building ZINC001515902660 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902660' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902660 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515902660 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902660/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902660 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 436) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@@H]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2F)C[C@@H](C)O1) `ZINC001515902660.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515902660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001515902660 none C[C@@H]1CN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2F)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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 10, 10, 10, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 10, 10, 2, 3, 1, 3, 10, 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, 46]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902660 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902660/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902660 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 437) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@@H]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2F)C[C@@H](C)O1) `ZINC001515902660.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515902660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902660/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001515902660 none C[C@@H]1CN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2F)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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 10, 10, 10, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 10, 10, 10, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 10, 10, 2, 3, 1, 3, 10, 47, 47, 47, 47, 47] 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: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902660 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515902660 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902660/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902660/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515902660 Building ZINC001515983822 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515983822' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515983822 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515983822 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515983822/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515983822 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/438 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(OCc2ccccc2)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c1) `ZINC001515983822.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515983822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515983822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001515983822 none COC(=O)c1ccc(OCc2ccccc2)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 6, 6, 6, 6, 6, 12, 28, 36, 36, 30, 36, 36, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 6, 10, 10, 10, 6, 6, 28, 28, 36, 36, 36, 36, 36, 4, 7, 7, 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]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515983822 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515983822/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515983822 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 439) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/439 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/439' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(OCc2ccccc2)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c1) `ZINC001515983822.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515983822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515983822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001515983822 none COC(=O)c1ccc(OCc2ccccc2)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 13, 6, 6, 6, 6, 6, 13, 31, 37, 37, 33, 37, 37, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 6, 13, 13, 13, 6, 6, 31, 31, 37, 37, 37, 37, 37, 4, 5, 5, 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]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515983822 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515983822 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515983822/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515983822/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515983822 Building ZINC001515983822 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515983822' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515983822 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001515983822 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515983822/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515983822 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 438) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COC(=O)c1ccc(OCc2ccccc2)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c1) `ZINC001515983822.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001515983822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515983822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001515983822 none COC(=O)c1ccc(OCc2ccccc2)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 6, 6, 6, 6, 6, 12, 28, 36, 36, 30, 36, 36, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 6, 10, 10, 10, 6, 6, 28, 28, 36, 36, 36, 36, 36, 4, 7, 7, 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]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515983822 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515983822/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515983822 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 439) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COC(=O)c1ccc(OCc2ccccc2)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c1) `ZINC001515983822.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001515983822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515983822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001515983822 none COC(=O)c1ccc(OCc2ccccc2)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 13, 6, 6, 6, 6, 6, 13, 31, 37, 37, 33, 37, 37, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 6, 13, 13, 13, 6, 6, 31, 31, 37, 37, 37, 37, 37, 4, 5, 5, 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]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515983822 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001515983822 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515983822/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515983822/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001515983822 Building ZINC001516134508 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516134508' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516134508 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516134508 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516134508/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516134508 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/440 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Br)c(F)cc1Cl)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001516134508.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516134508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516134508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001516134508 none O=C(Nc1cc(Br)c(F)cc1Cl)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', '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, 17, 1, 15, 1, 1, 16, 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: [7, 1, 7, 7, 29, 29, 29, 16, 17, 29, 29, 29, 1, 1, 1, 12, 12, 12, 12, 12, 7, 29, 29, 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: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516134508 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516134508/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516134508 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 441) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/441 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/441' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Br)c(F)cc1Cl)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001516134508.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516134508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516134508/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001516134508 none O=C(Nc1cc(Br)c(F)cc1Cl)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', '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, 17, 1, 15, 1, 1, 16, 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: [7, 1, 7, 7, 29, 29, 29, 9, 13, 29, 29, 29, 1, 1, 1, 12, 12, 12, 12, 12, 7, 29, 29, 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: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516134508 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516134508 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516134508/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516134508/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516134508 Building ZINC001516134508 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516134508' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516134508 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516134508 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516134508/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516134508 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 440) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1cc(Br)c(F)cc1Cl)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001516134508.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516134508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516134508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001516134508 none O=C(Nc1cc(Br)c(F)cc1Cl)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', '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, 17, 1, 15, 1, 1, 16, 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: [7, 1, 7, 7, 29, 29, 29, 16, 17, 29, 29, 29, 1, 1, 1, 12, 12, 12, 12, 12, 7, 29, 29, 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: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516134508 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516134508/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516134508 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 441) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1cc(Br)c(F)cc1Cl)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001516134508.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516134508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516134508/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001516134508 none O=C(Nc1cc(Br)c(F)cc1Cl)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', '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, 17, 1, 15, 1, 1, 16, 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: [7, 1, 7, 7, 29, 29, 29, 9, 13, 29, 29, 29, 1, 1, 1, 12, 12, 12, 12, 12, 7, 29, 29, 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: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516134508 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516134508 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516134508/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516134508/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516134508 Building ZINC001516187228 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516187228' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516187228 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516187228 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516187228/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516187228 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/442 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCn1ccnc1c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC001516187228.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516187228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516187228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001516187228 none CCCCn1ccnc1c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 33, 16, 16, 16, 16, 16, 7, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 7, 38, 38, 38, 38, 38, 38, 38, 33, 33, 16, 16, 7, 7, 7, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 7] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516187228 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516187228/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516187228 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 443) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/443 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/443' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCn1ccnc1c1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC001516187228.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516187228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516187228/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001516187228 none CCCCn1ccnc1c1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 16, 16, 16, 16, 16, 7, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 7, 37, 37, 37, 37, 37, 37, 37, 32, 32, 16, 16, 7, 7, 7, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 7] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516187228 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516187228 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516187228/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516187228/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516187228 Building ZINC001516187228 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516187228' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516187228 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516187228 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516187228/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516187228 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 442) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCCCn1ccnc1c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC001516187228.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516187228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516187228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001516187228 none CCCCn1ccnc1c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 33, 16, 16, 16, 16, 16, 7, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 7, 38, 38, 38, 38, 38, 38, 38, 33, 33, 16, 16, 7, 7, 7, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 7] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516187228 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516187228/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516187228 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 443) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCCCn1ccnc1c1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC001516187228.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516187228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516187228/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001516187228 none CCCCn1ccnc1c1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 16, 16, 16, 16, 16, 7, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 7, 37, 37, 37, 37, 37, 37, 37, 32, 32, 16, 16, 7, 7, 7, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 7] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516187228 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516187228 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516187228/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516187228/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516187228 Building ZINC001516255923 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516255923' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516255923 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516255923 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516255923/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516255923 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/444 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(Oc2ncccc2CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)cc1) `ZINC001516255923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516255923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516255923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001516255923 none CCCOc1ccc(Oc2ncccc2CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 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, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 31, 31, 20, 16, 16, 16, 16, 16, 16, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 31, 31, 49, 49, 49, 49, 49, 49, 49, 31, 31, 16, 16, 16, 12, 12, 2, 4, 4, 31, 31] 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: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516255923 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516255923/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516255923 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 445) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/445 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/445' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(Oc2ncccc2CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)cc1) `ZINC001516255923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516255923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516255923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001516255923 none CCCOc1ccc(Oc2ncccc2CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 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, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 33, 33, 33, 22, 17, 17, 17, 17, 17, 17, 12, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 33, 33, 49, 49, 49, 49, 49, 49, 49, 33, 33, 17, 17, 17, 12, 12, 2, 3, 3, 33, 33] 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: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516255923 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516255923 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516255923/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516255923/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516255923 Building ZINC001516255923 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516255923' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516255923 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516255923 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516255923/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516255923 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 444) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCCOc1ccc(Oc2ncccc2CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)cc1) `ZINC001516255923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516255923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516255923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001516255923 none CCCOc1ccc(Oc2ncccc2CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 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, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 31, 31, 20, 16, 16, 16, 16, 16, 16, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 31, 31, 49, 49, 49, 49, 49, 49, 49, 31, 31, 16, 16, 16, 12, 12, 2, 4, 4, 31, 31] 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: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516255923 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516255923/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516255923 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 445) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCCOc1ccc(Oc2ncccc2CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)cc1) `ZINC001516255923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516255923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516255923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001516255923 none CCCOc1ccc(Oc2ncccc2CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)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.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 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, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 33, 33, 33, 22, 17, 17, 17, 17, 17, 17, 12, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 33, 33, 49, 49, 49, 49, 49, 49, 49, 33, 33, 17, 17, 17, 12, 12, 2, 3, 3, 33, 33] 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: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516255923 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516255923 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516255923/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516255923/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516255923 Building ZINC001516397169 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516397169' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516397169 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516397169 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516397169/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516397169 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/446 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/446' -> `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)Cc1ccc(C(F)(F)F)cc1) `ZINC001516397169.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516397169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516397169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001516397169 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)Cc1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 6, 12, 12, 12, 12, 12, 12, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 174 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516397169 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516397169/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516397169 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 447) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/447 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/447' -> `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)Cc1ccc(C(F)(F)F)cc1) `ZINC001516397169.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516397169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516397169/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001516397169 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)Cc1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 2, 2, 2, 5, 5, 3, 5, 5, 2, 2, 2, 6, 12, 12, 12, 12, 12, 12, 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]) total number of confs: 173 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516397169 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516397169 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516397169/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516397169/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516397169 Building ZINC001516397169 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516397169' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516397169 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516397169 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516397169/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516397169 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 446) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)Cc1ccc(C(F)(F)F)cc1) `ZINC001516397169.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516397169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516397169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001516397169 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)Cc1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 6, 12, 12, 12, 12, 12, 12, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 174 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516397169 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516397169/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516397169 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 447) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)Cc1ccc(C(F)(F)F)cc1) `ZINC001516397169.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516397169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516397169/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001516397169 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)Cc1ccc(C(F)(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 2, 2, 2, 5, 5, 3, 5, 5, 2, 2, 2, 6, 12, 12, 12, 12, 12, 12, 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]) total number of confs: 173 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516397169 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516397169 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516397169/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516397169/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516397169 Building ZINC001516518287 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516518287' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516518287 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516518287 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516518287/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516518287 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/448 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Br)cc2c2nc(C3CC3)no2)c1) `ZINC001516518287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516518287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516518287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001516518287 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Br)cc2c2nc(C3CC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 1, 5, 5, 5, 8, 12, 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, 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: [4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22, 28, 28, 22, 22, 4, 4, 4, 4, 2, 4, 4, 3, 6, 6, 6, 28, 28, 28, 28, 28, 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516518287 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516518287/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516518287 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 449) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/449 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/449' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Br)cc2c2nc(C3CC3)no2)c1) `ZINC001516518287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516518287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516518287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001516518287 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Br)cc2c2nc(C3CC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 1, 5, 5, 5, 8, 12, 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, 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: [4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22, 30, 30, 22, 22, 4, 4, 4, 4, 2, 4, 4, 3, 6, 6, 6, 30, 30, 30, 30, 30, 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516518287 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516518287 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516518287/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516518287/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516518287 Building ZINC001516518287 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516518287' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516518287 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516518287 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516518287/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516518287 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 448) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Br)cc2c2nc(C3CC3)no2)c1) `ZINC001516518287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516518287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516518287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001516518287 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Br)cc2c2nc(C3CC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 1, 5, 5, 5, 8, 12, 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, 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: [4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22, 28, 28, 22, 22, 4, 4, 4, 4, 2, 4, 4, 3, 6, 6, 6, 28, 28, 28, 28, 28, 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516518287 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516518287/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516518287 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 449) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Br)cc2c2nc(C3CC3)no2)c1) `ZINC001516518287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516518287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516518287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001516518287 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Br)cc2c2nc(C3CC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 1, 5, 5, 5, 8, 12, 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, 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: [4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22, 30, 30, 22, 22, 4, 4, 4, 4, 2, 4, 4, 3, 6, 6, 6, 30, 30, 30, 30, 30, 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516518287 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516518287 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516518287/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516518287/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516518287 Building ZINC001516576418 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576418' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576418 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516576418 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576418/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576418 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/450 `/scratch/xiaobo/12845/xbi-8058088.35/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)N1CCc2ccccc2[C@@H]1C) `ZINC001516576418.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516576418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001516576418 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccccc2[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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', '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'] dock atom type numbers: [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, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 23, 23, 16, 23, 23, 23, 23, 23, 23, 4, 4, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 23, 23, 20, 23, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 56 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576418 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576418/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576418 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 451) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/451 `/scratch/xiaobo/12845/xbi-8058088.35/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)N1CCc2ccccc2[C@@H]1C) `ZINC001516576418.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516576418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576418/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001516576418 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccccc2[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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', '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'] dock atom type numbers: [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, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 28, 28, 3, 28, 28, 28, 28, 28, 28, 3, 3, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 28, 28, 3, 28, 3, 3, 3, 8, 8, 8, 8, 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, 53]) total number of confs: 79 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576418 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516576418 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576418/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576418/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576418 Building ZINC001516576418 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576418' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576418 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516576418 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576418/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576418 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 450) grep: /scratch/xiaobo/12845/xbi-8058088.35/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)N1CCc2ccccc2[C@@H]1C) `ZINC001516576418.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516576418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001516576418 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccccc2[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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', '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'] dock atom type numbers: [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, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 23, 23, 16, 23, 23, 23, 23, 23, 23, 4, 4, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 23, 23, 20, 23, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 56 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576418 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576418/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576418 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 451) grep: /scratch/xiaobo/12845/xbi-8058088.35/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)N1CCc2ccccc2[C@@H]1C) `ZINC001516576418.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516576418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576418/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001516576418 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccccc2[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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', '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'] dock atom type numbers: [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, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 28, 28, 3, 28, 28, 28, 28, 28, 28, 3, 3, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 28, 28, 3, 28, 3, 3, 3, 8, 8, 8, 8, 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, 53]) total number of confs: 79 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576418 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516576418 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576418/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576418/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576418 Building ZINC001516576419 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576419' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576419 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516576419 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576419/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576419 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/452 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/452' -> `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)N1CCc2ccccc2[C@H]1C) `ZINC001516576419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516576419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001516576419 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccccc2[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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', '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'] dock atom type numbers: [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, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 28, 28, 3, 28, 28, 28, 28, 28, 28, 3, 3, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 28, 28, 4, 28, 3, 3, 3, 8, 8, 8, 8, 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, 53]) total number of confs: 81 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576419 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576419/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576419 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 453) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/453 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/453' -> `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)N1CCc2ccccc2[C@H]1C) `ZINC001516576419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516576419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001516576419 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccccc2[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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', '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'] dock atom type numbers: [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, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 22, 22, 4, 22, 22, 22, 22, 22, 22, 4, 4, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 22, 22, 4, 22, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 67 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576419 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516576419 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576419/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576419/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576419 Building ZINC001516576419 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576419' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576419 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516576419 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576419/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576419 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 452) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccccc2[C@H]1C) `ZINC001516576419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516576419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001516576419 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2ccccc2[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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', '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'] dock atom type numbers: [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, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 28, 28, 3, 28, 28, 28, 28, 28, 28, 3, 3, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 28, 28, 4, 28, 3, 3, 3, 8, 8, 8, 8, 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, 53]) total number of confs: 81 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576419 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576419/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576419 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 453) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccccc2[C@H]1C) `ZINC001516576419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516576419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001516576419 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2ccccc2[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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', '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'] dock atom type numbers: [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, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 22, 22, 4, 22, 22, 22, 22, 22, 22, 4, 4, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 22, 22, 4, 22, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 67 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576419 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516576419 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576419/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576419/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516576419 Building ZINC001516577399 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516577399' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516577399 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516577399 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516577399/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516577399 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/454 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1) `ZINC001516577399.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516577399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516577399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001516577399 none O=C(Nc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', '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', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 18, 18, 18, 14, 18, 18, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 28, 34, 34, 34, 34, 34, 28, 18, 18, 18, 18, 4, 7, 7, 34, 34, 34, 34, 34] 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516577399 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516577399/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516577399 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 455) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/455 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/455' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1) `ZINC001516577399.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516577399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516577399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001516577399 none O=C(Nc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', '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', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 18, 18, 18, 14, 18, 18, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 28, 34, 34, 28, 34, 34, 28, 18, 18, 18, 18, 4, 7, 7, 34, 34, 28, 34, 34] 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516577399 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516577399 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516577399/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516577399/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516577399 Building ZINC001516577399 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516577399' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516577399 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516577399 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516577399/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516577399 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 454) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1) `ZINC001516577399.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516577399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516577399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001516577399 none O=C(Nc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', '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', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 18, 18, 18, 14, 18, 18, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 28, 34, 34, 34, 34, 34, 28, 18, 18, 18, 18, 4, 7, 7, 34, 34, 34, 34, 34] 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516577399 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516577399/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516577399 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 455) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1) `ZINC001516577399.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516577399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516577399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001516577399 none O=C(Nc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', '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', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 18, 18, 18, 14, 18, 18, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 28, 34, 34, 28, 34, 34, 28, 18, 18, 18, 18, 4, 7, 7, 34, 34, 28, 34, 34] 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516577399 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516577399 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516577399/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516577399/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516577399 Building ZINC001516589239 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516589239' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516589239 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516589239 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516589239/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516589239 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/456 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(Cc2ccc(F)cc2)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001516589239.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516589239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516589239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001516589239 none O=C(Nc1ncc(Cc2ccc(F)cc2)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1 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', 'F', '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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 5, 1, 1, 1, 1, 15, 1, 1, 14, 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, 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, 6, 6, 6, 6, 30, 32, 32, 32, 32, 32, 32, 6, 1, 1, 1, 7, 7, 7, 7, 7, 4, 6, 30, 30, 32, 32, 32, 32, 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516589239 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516589239/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516589239 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 457) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/457 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/457' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(Cc2ccc(F)cc2)s1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001516589239.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516589239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516589239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001516589239 none O=C(Nc1ncc(Cc2ccc(F)cc2)s1)[C@]([O-])([SiH3])c1ccc(Br)s1 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', 'F', '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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 5, 1, 1, 1, 1, 15, 1, 1, 14, 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, 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, 6, 6, 6, 6, 30, 32, 32, 32, 32, 32, 32, 6, 1, 1, 1, 7, 7, 7, 7, 7, 4, 6, 30, 30, 32, 32, 32, 32, 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516589239 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516589239 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516589239/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516589239/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516589239 Building ZINC001516589239 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516589239' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516589239 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516589239 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516589239/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516589239 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 456) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(Nc1ncc(Cc2ccc(F)cc2)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001516589239.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516589239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516589239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001516589239 none O=C(Nc1ncc(Cc2ccc(F)cc2)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1 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', 'F', '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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 5, 1, 1, 1, 1, 15, 1, 1, 14, 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, 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, 6, 6, 6, 6, 30, 32, 32, 32, 32, 32, 32, 6, 1, 1, 1, 7, 7, 7, 7, 7, 4, 6, 30, 30, 32, 32, 32, 32, 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516589239 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516589239/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516589239 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 457) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(Nc1ncc(Cc2ccc(F)cc2)s1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001516589239.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516589239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516589239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001516589239 none O=C(Nc1ncc(Cc2ccc(F)cc2)s1)[C@]([O-])([SiH3])c1ccc(Br)s1 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', 'F', '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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 5, 1, 1, 1, 1, 15, 1, 1, 14, 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, 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, 6, 6, 6, 6, 30, 32, 32, 32, 32, 32, 32, 6, 1, 1, 1, 7, 7, 7, 7, 7, 4, 6, 30, 30, 32, 32, 32, 32, 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516589239 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516589239 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516589239/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516589239/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516589239 Building ZINC001516614536 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614536' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614536 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516614536 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614536/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614536 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/458 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccccc1[C@@H](CC(C)C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001516614536.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516614536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001516614536 none CCOc1ccccc1[C@@H](CC(C)C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C 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.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 16, 8, 8, 8, 4, 8, 8, 2, 2, 2, 2, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 23, 23, 23, 23, 23, 8, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 106 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614536 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614536/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614536 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 459) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/459 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/459' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccccc1[C@@H](CC(C)C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001516614536.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516614536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614536/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001516614536 none CCOc1ccccc1[C@@H](CC(C)C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C 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.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 19, 11, 11, 11, 7, 11, 11, 4, 2, 4, 4, 6, 6, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 6, 8, 8, 4, 4, 26, 26, 26, 26, 26, 11, 11, 11, 11, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 123 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614536 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516614536 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614536/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614536/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614536 Building ZINC001516614536 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614536' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614536 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516614536 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614536/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614536 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 458) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOc1ccccc1[C@@H](CC(C)C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001516614536.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516614536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001516614536 none CCOc1ccccc1[C@@H](CC(C)C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C 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.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 16, 8, 8, 8, 4, 8, 8, 2, 2, 2, 2, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 23, 23, 23, 23, 23, 8, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 106 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614536 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614536/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614536 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 459) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOc1ccccc1[C@@H](CC(C)C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001516614536.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516614536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614536/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001516614536 none CCOc1ccccc1[C@@H](CC(C)C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C 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.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 19, 11, 11, 11, 7, 11, 11, 4, 2, 4, 4, 6, 6, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 6, 8, 8, 4, 4, 26, 26, 26, 26, 26, 11, 11, 11, 11, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 123 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614536 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516614536 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614536/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614536/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614536 Building ZINC001516614537 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614537' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614537 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516614537 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614537/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614537 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/460 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccccc1[C@H](CC(C)C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001516614537.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516614537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001516614537 none CCOc1ccccc1[C@H](CC(C)C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C 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.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 9, 9, 9, 6, 9, 9, 3, 2, 3, 3, 7, 7, 7, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 29, 29, 29, 29, 29, 9, 9, 9, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 131 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614537 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614537/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614537 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 461) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/461 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/461' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccccc1[C@H](CC(C)C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001516614537.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516614537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614537/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001516614537 none CCOc1ccccc1[C@H](CC(C)C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C 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.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 10, 10, 4, 2, 4, 4, 7, 7, 7, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 4, 4, 28, 28, 28, 28, 28, 10, 10, 10, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 119 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614537 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516614537 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614537/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614537/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614537 Building ZINC001516614537 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614537' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614537 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516614537 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614537/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614537 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 460) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOc1ccccc1[C@H](CC(C)C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001516614537.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516614537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001516614537 none CCOc1ccccc1[C@H](CC(C)C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C 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.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 9, 9, 9, 6, 9, 9, 3, 2, 3, 3, 7, 7, 7, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 29, 29, 29, 29, 29, 9, 9, 9, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 131 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614537 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614537/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614537 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 461) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOc1ccccc1[C@H](CC(C)C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001516614537.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516614537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614537/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001516614537 none CCOc1ccccc1[C@H](CC(C)C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C 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.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 10, 10, 4, 2, 4, 4, 7, 7, 7, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 4, 4, 28, 28, 28, 28, 28, 10, 10, 10, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 119 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614537 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516614537 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614537/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614537/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516614537 Building ZINC001516619539 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516619539' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516619539 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516619539 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516619539/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516619539 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/462 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1cccs1)c1ccc(Br)cc1) `ZINC001516619539.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516619539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516619539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001516619539 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1cccs1)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 14, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 8, 21, 37, 37, 37, 37, 8, 17, 17, 9, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 21, 21, 37, 37, 37, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516619539 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516619539/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516619539 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 463) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/463 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/463' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1cccs1)c1ccc(Br)cc1) `ZINC001516619539.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516619539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516619539/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001516619539 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1cccs1)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 14, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 8, 21, 39, 39, 39, 39, 8, 17, 17, 10, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 21, 21, 39, 39, 39, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516619539 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516619539 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516619539/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516619539/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516619539 Building ZINC001516619539 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516619539' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516619539 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516619539 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516619539/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516619539 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 462) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1cccs1)c1ccc(Br)cc1) `ZINC001516619539.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516619539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516619539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001516619539 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(Cc1cccs1)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 14, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 8, 21, 37, 37, 37, 37, 8, 17, 17, 9, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 21, 21, 37, 37, 37, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516619539 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516619539/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516619539 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 463) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1cccs1)c1ccc(Br)cc1) `ZINC001516619539.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516619539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516619539/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001516619539 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(Cc1cccs1)c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 14, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 8, 21, 39, 39, 39, 39, 8, 17, 17, 10, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 21, 21, 39, 39, 39, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516619539 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516619539 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516619539/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516619539/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516619539 Building ZINC001516708409 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516708409' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516708409 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516708409 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516708409/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516708409 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/464 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)NC2CCCCC2)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001516708409.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516708409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516708409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001516708409 none Cc1cc(C(=O)NC2CCCCC2)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', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 18, 18, 31, 48, 48, 48, 48, 48, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 5, 18, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 2, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516708409 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516708409/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516708409 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 465) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/465 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/465' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)NC2CCCCC2)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001516708409.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516708409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516708409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001516708409 none Cc1cc(C(=O)NC2CCCCC2)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', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 5, 17, 17, 30, 46, 46, 46, 46, 46, 5, 5, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 17, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 5, 5, 2, 5, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516708409 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516708409 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516708409/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516708409/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516708409 Building ZINC001516708409 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516708409' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516708409 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516708409 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516708409/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516708409 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 464) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1cc(C(=O)NC2CCCCC2)ccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001516708409.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516708409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516708409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001516708409 none Cc1cc(C(=O)NC2CCCCC2)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', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 18, 18, 31, 48, 48, 48, 48, 48, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 5, 18, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5, 2, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516708409 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516708409/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516708409 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 465) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1cc(C(=O)NC2CCCCC2)ccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001516708409.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516708409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516708409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001516708409 none Cc1cc(C(=O)NC2CCCCC2)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', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 5, 17, 17, 30, 46, 46, 46, 46, 46, 5, 5, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 17, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 5, 5, 2, 5, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516708409 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516708409 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516708409/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516708409/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516708409 Building ZINC001516778081 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516778081' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516778081 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516778081 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516778081/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516778081 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/466 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/466' -> `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(C)cc1Br) `ZINC001516778081.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516778081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516778081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001516778081 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(C)cc(C)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.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 17, 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 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 4, 14, 14, 4, 4, 1, 1, 1, 1, 9, 9, 9, 30, 30, 30, 14, 17, 30, 30, 30, 4, 4, 4, 14, 14, 4, 14, 14, 4, 4, 4, 9, 30, 30, 30, 30, 30, 30, 30, 30] 49 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 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: 186 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516778081 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516778081/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516778081 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 467) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/467 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/467' -> `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(C)cc1Br) `ZINC001516778081.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516778081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516778081/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001516778081 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(C)cc(C)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.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 17, 17, 6, 17, 17, 6, 6, 1, 1, 1, 1, 8, 8, 8, 26, 26, 26, 8, 16, 26, 26, 26, 6, 6, 6, 17, 17, 6, 17, 17, 6, 6, 6, 8, 26, 26, 26, 26, 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]) total number of confs: 190 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516778081 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516778081 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516778081/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516778081/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516778081 Building ZINC001516778081 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516778081' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516778081 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516778081 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516778081/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516778081 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 466) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(C)cc(C)cc1Br) `ZINC001516778081.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516778081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516778081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001516778081 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(C)cc(C)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.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 17, 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 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 4, 14, 14, 4, 4, 1, 1, 1, 1, 9, 9, 9, 30, 30, 30, 14, 17, 30, 30, 30, 4, 4, 4, 14, 14, 4, 14, 14, 4, 4, 4, 9, 30, 30, 30, 30, 30, 30, 30, 30] 49 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 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: 186 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516778081 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516778081/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516778081 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 467) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(C)cc(C)cc1Br) `ZINC001516778081.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516778081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516778081/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001516778081 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(C)cc(C)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.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 17, 17, 6, 17, 17, 6, 6, 1, 1, 1, 1, 8, 8, 8, 26, 26, 26, 8, 16, 26, 26, 26, 6, 6, 6, 17, 17, 6, 17, 17, 6, 6, 6, 8, 26, 26, 26, 26, 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]) total number of confs: 190 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516778081 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516778081 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516778081/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516778081/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516778081 Building ZINC001516780617 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516780617' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516780617 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516780617 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516780617/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516780617 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/468 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1CSc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001516780617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516780617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516780617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001516780617 none COc1ccccc1CSc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 12, 1, 1, 1, 1, 1, 1, 5, 14, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 33, 29, 33, 33, 24, 9, 5, 5, 5, 4, 5, 5, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 39, 39, 39, 33, 33, 33, 33, 24, 24, 5, 5, 5, 5, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516780617 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516780617/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516780617 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 469) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/469 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/469' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1CSc1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001516780617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516780617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516780617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001516780617 none COc1ccccc1CSc1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 12, 1, 1, 1, 1, 1, 1, 5, 14, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 33, 33, 33, 28, 33, 33, 23, 8, 4, 4, 4, 3, 4, 4, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 40, 40, 40, 33, 33, 33, 33, 23, 23, 4, 4, 4, 4, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516780617 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516780617 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516780617/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516780617/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516780617 Building ZINC001516780617 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516780617' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516780617 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516780617 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516780617/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516780617 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 468) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccccc1CSc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001516780617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516780617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516780617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001516780617 none COc1ccccc1CSc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 12, 1, 1, 1, 1, 1, 1, 5, 14, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 33, 29, 33, 33, 24, 9, 5, 5, 5, 4, 5, 5, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 39, 39, 39, 33, 33, 33, 33, 24, 24, 5, 5, 5, 5, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516780617 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516780617/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516780617 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 469) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccccc1CSc1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001516780617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516780617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516780617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001516780617 none COc1ccccc1CSc1ccccc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.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', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 12, 1, 1, 1, 1, 1, 1, 5, 14, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 33, 33, 33, 28, 33, 33, 23, 8, 4, 4, 4, 3, 4, 4, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 40, 40, 40, 33, 33, 33, 33, 23, 23, 4, 4, 4, 4, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516780617 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516780617 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516780617/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516780617/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516780617 Building ZINC001516804635 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516804635' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516804635 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516804635 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516804635/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516804635 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/470 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/470' -> `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)N1CCCSc2ccc(Cl)cc21) `ZINC001516804635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516804635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516804635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001516804635 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCSc2ccc(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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 14, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 4, 14, 14, 4, 4, 1, 1, 1, 2, 12, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 14, 14, 4, 14, 14, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 79 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516804635 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516804635/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516804635 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 471) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/471 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/471' -> `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)N1CCCSc2ccc(Cl)cc21) `ZINC001516804635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516804635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516804635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001516804635 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCSc2ccc(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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 14, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 3, 3, 1, 1, 1, 2, 12, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 3, 12, 12, 3, 12, 12, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22] 46 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 71 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516804635 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516804635 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516804635/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516804635/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516804635 Building ZINC001516804635 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516804635' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516804635 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516804635 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516804635/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516804635 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 470) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/470: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCSc2ccc(Cl)cc21) `ZINC001516804635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516804635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516804635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001516804635 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCSc2ccc(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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 14, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 4, 14, 14, 4, 4, 1, 1, 1, 2, 12, 16, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 14, 14, 4, 14, 14, 4, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 79 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516804635 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516804635/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516804635 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 471) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/471: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCSc2ccc(Cl)cc21) `ZINC001516804635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516804635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516804635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001516804635 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCSc2ccc(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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 14, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 3, 3, 1, 1, 1, 2, 12, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 3, 12, 12, 3, 12, 12, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22] 46 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 71 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516804635 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516804635 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516804635/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516804635/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516804635 Building ZINC001516897524 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897524' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897524 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516897524 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897524/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897524 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/472 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](Cc1cccc(Br)c1)CC1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001516897524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516897524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001516897524 none O=C(N[C@H](Cc1cccc(Br)c1)CC1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 17, 1, 5, 5, 5, 5, 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] 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, 6, 6, 12, 18, 18, 18, 18, 18, 18, 6, 13, 19, 19, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 12, 12, 18, 18, 18, 18, 14, 14, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4, 4, 4, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897524 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897524/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897524 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 473) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/473 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/473' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](Cc1cccc(Br)c1)CC1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001516897524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516897524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001516897524 none O=C(N[C@H](Cc1cccc(Br)c1)CC1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 17, 1, 5, 5, 5, 5, 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] 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, 5, 5, 9, 15, 15, 15, 15, 15, 15, 5, 10, 15, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 15, 15, 15, 15, 11, 11, 15, 15, 15, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897524 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516897524 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897524/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897524/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897524 Building ZINC001516897524 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897524' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897524 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516897524 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897524/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897524 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 472) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(N[C@H](Cc1cccc(Br)c1)CC1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001516897524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516897524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001516897524 none O=C(N[C@H](Cc1cccc(Br)c1)CC1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 17, 1, 5, 5, 5, 5, 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] 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, 6, 6, 12, 18, 18, 18, 18, 18, 18, 6, 13, 19, 19, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 12, 12, 18, 18, 18, 18, 14, 14, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4, 4, 4, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897524 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897524/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897524 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 473) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(N[C@H](Cc1cccc(Br)c1)CC1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001516897524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516897524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001516897524 none O=C(N[C@H](Cc1cccc(Br)c1)CC1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 17, 1, 5, 5, 5, 5, 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] 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, 5, 5, 9, 15, 15, 15, 15, 15, 15, 5, 10, 15, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 15, 15, 15, 15, 11, 11, 15, 15, 15, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897524 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516897524 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897524/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897524/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897524 Building ZINC001516897526 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897526' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897526 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516897526 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897526/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897526 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/474 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](Cc1cccc(Br)c1)CC1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001516897526.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516897526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001516897526 none O=C(N[C@@H](Cc1cccc(Br)c1)CC1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 17, 1, 5, 5, 5, 5, 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] 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, 5, 5, 10, 17, 17, 17, 17, 17, 17, 5, 10, 17, 17, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 17, 17, 17, 17, 11, 11, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 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, 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/12845/xbi-8058088.35/working/building/ZINC001516897526 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897526/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897526 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 475) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/475 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/475' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](Cc1cccc(Br)c1)CC1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001516897526.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516897526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897526/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001516897526 none O=C(N[C@@H](Cc1cccc(Br)c1)CC1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 17, 1, 5, 5, 5, 5, 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] 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, 6, 6, 12, 18, 18, 18, 18, 18, 18, 6, 13, 20, 20, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 12, 12, 18, 18, 18, 18, 15, 15, 20, 20, 20, 20, 20, 4, 4, 4, 4, 4, 4, 4, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897526 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516897526 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897526/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897526/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897526 Building ZINC001516897526 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897526' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897526 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516897526 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897526/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897526 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 474) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N[C@@H](Cc1cccc(Br)c1)CC1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001516897526.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516897526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001516897526 none O=C(N[C@@H](Cc1cccc(Br)c1)CC1CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 17, 1, 5, 5, 5, 5, 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] 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, 5, 5, 10, 17, 17, 17, 17, 17, 17, 5, 10, 17, 17, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 17, 17, 17, 17, 11, 11, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 4, 4, 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, 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/12845/xbi-8058088.35/working/building/ZINC001516897526 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897526/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897526 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 475) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N[C@@H](Cc1cccc(Br)c1)CC1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001516897526.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516897526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897526/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001516897526 none O=C(N[C@@H](Cc1cccc(Br)c1)CC1CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 17, 1, 5, 5, 5, 5, 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] 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, 6, 6, 12, 18, 18, 18, 18, 18, 18, 6, 13, 20, 20, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 12, 12, 18, 18, 18, 18, 15, 15, 20, 20, 20, 20, 20, 4, 4, 4, 4, 4, 4, 4, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897526 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516897526 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897526/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897526/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516897526 Building ZINC001516926234 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926234' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926234 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516926234 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926234/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926234 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/476 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(Cl)c(Cl)c1) `ZINC001516926234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516926234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001516926234 none COC(=O)[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 13, 4, 9, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 33, 33, 19, 33, 33, 33, 33, 13, 13, 13, 9, 9, 9, 4, 3, 1, 3, 33, 33, 33] 50 rigid atoms, others: [7, 9, 10, 11] 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926234 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926234/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926234 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 477) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/477 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/477' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@](C)(NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(Cl)c(Cl)c1) `ZINC001516926234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516926234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001516926234 none COC(=O)[C@](C)(NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 10, 17, 4, 10, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 10, 32, 32, 18, 32, 32, 32, 32, 17, 17, 17, 10, 10, 10, 4, 3, 1, 3, 32, 32, 32] 50 rigid atoms, others: [7, 9, 10, 11] 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]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926234 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516926234 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926234/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926234/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926234 Building ZINC001516926234 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926234' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926234 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516926234 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926234/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926234 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 476) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COC(=O)[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(Cl)c(Cl)c1) `ZINC001516926234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516926234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001516926234 none COC(=O)[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 13, 4, 9, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 33, 33, 19, 33, 33, 33, 33, 13, 13, 13, 9, 9, 9, 4, 3, 1, 3, 33, 33, 33] 50 rigid atoms, others: [7, 9, 10, 11] 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926234 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926234/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926234 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 477) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COC(=O)[C@](C)(NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(Cl)c(Cl)c1) `ZINC001516926234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516926234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001516926234 none COC(=O)[C@](C)(NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 10, 17, 4, 10, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 10, 32, 32, 18, 32, 32, 32, 32, 17, 17, 17, 10, 10, 10, 4, 3, 1, 3, 32, 32, 32] 50 rigid atoms, others: [7, 9, 10, 11] 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]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926234 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516926234 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926234/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926234/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926234 Building ZINC001516926313 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926313' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926313 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516926313 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926313/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926313 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/478 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(Cl)c(Cl)c1) `ZINC001516926313.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516926313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001516926313 none COC(=O)[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 16, 4, 9, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 32, 32, 18, 32, 32, 32, 32, 16, 16, 16, 9, 9, 9, 4, 3, 1, 3, 32, 32, 32] 50 rigid atoms, others: [7, 9, 10, 11] 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]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926313 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926313/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926313 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 479) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/479 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/479' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(Cl)c(Cl)c1) `ZINC001516926313.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516926313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926313/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001516926313 none COC(=O)[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 13, 4, 9, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 34, 34, 20, 34, 34, 34, 34, 13, 13, 13, 9, 9, 9, 4, 3, 1, 3, 34, 34, 34] 50 rigid atoms, others: [7, 9, 10, 11] 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926313 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516926313 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926313/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926313/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926313 Building ZINC001516926313 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926313' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926313 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516926313 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926313/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926313 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 478) grep: /scratch/xiaobo/12845/xbi-8058088.35/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)[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(Cl)c(Cl)c1) `ZINC001516926313.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516926313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001516926313 none COC(=O)[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 16, 4, 9, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 32, 32, 18, 32, 32, 32, 32, 16, 16, 16, 9, 9, 9, 4, 3, 1, 3, 32, 32, 32] 50 rigid atoms, others: [7, 9, 10, 11] 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]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926313 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926313/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926313 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 479) grep: /scratch/xiaobo/12845/xbi-8058088.35/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)[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(Cl)c(Cl)c1) `ZINC001516926313.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516926313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926313/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001516926313 none COC(=O)[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 13, 4, 9, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 34, 34, 20, 34, 34, 34, 34, 13, 13, 13, 9, 9, 9, 4, 3, 1, 3, 34, 34, 34] 50 rigid atoms, others: [7, 9, 10, 11] 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926313 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516926313 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926313/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926313/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516926313 Building ZINC001516975288 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975288' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975288 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516975288 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975288/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975288 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/480 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccc(Oc2ccccc2)c(F)c1) `ZINC001516975288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516975288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001516975288 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccc(Oc2ccccc2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 12, 12, 12, 12, 38, 38, 38, 38, 38, 38, 12, 12, 12, 4, 4, 4, 2, 6, 6, 6, 6, 6, 6, 6, 12, 12, 38, 38, 38, 38, 38, 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: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975288 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975288/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975288 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 481) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/481 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/481' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccc(Oc2ccccc2)c(F)c1) `ZINC001516975288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516975288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001516975288 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccc(Oc2ccccc2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 9, 9, 9, 9, 35, 36, 36, 35, 36, 36, 9, 9, 9, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 9, 9, 36, 36, 35, 36, 36, 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: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975288 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516975288 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975288/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975288/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975288 Building ZINC001516975288 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975288' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975288 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516975288 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975288/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975288 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 480) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccc(Oc2ccccc2)c(F)c1) `ZINC001516975288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516975288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001516975288 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccc(Oc2ccccc2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 12, 12, 12, 12, 38, 38, 38, 38, 38, 38, 12, 12, 12, 4, 4, 4, 2, 6, 6, 6, 6, 6, 6, 6, 12, 12, 38, 38, 38, 38, 38, 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: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975288 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975288/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975288 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 481) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccc(Oc2ccccc2)c(F)c1) `ZINC001516975288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516975288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001516975288 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccc(Oc2ccccc2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 9, 9, 9, 9, 35, 36, 36, 35, 36, 36, 9, 9, 9, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 9, 9, 36, 36, 35, 36, 36, 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: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975288 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516975288 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975288/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975288/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975288 Building ZINC001516975290 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975290' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975290 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516975290 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975290/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975290 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/482 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccc(Oc2ccccc2)c(F)c1) `ZINC001516975290.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516975290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001516975290 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccc(Oc2ccccc2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 9, 9, 9, 9, 35, 36, 36, 35, 36, 36, 9, 9, 9, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 9, 9, 36, 36, 36, 36, 36, 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: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975290 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975290/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975290 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 483) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/483 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/483' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccc(Oc2ccccc2)c(F)c1) `ZINC001516975290.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516975290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001516975290 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccc(Oc2ccccc2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 12, 12, 12, 12, 37, 37, 37, 37, 37, 37, 12, 12, 12, 4, 4, 4, 2, 6, 6, 6, 6, 6, 6, 6, 12, 12, 37, 37, 37, 37, 37, 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: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975290 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516975290 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975290/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975290/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975290 Building ZINC001516975290 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975290' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975290 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001516975290 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975290/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975290 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 482) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccc(Oc2ccccc2)c(F)c1) `ZINC001516975290.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001516975290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001516975290 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccc(Oc2ccccc2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 9, 9, 9, 9, 35, 36, 36, 35, 36, 36, 9, 9, 9, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 9, 9, 36, 36, 36, 36, 36, 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: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975290 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975290/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975290 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 483) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccc(Oc2ccccc2)c(F)c1) `ZINC001516975290.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001516975290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001516975290 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccc(Oc2ccccc2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 15, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 12, 12, 12, 12, 37, 37, 37, 37, 37, 37, 12, 12, 12, 4, 4, 4, 2, 6, 6, 6, 6, 6, 6, 6, 12, 12, 37, 37, 37, 37, 37, 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: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975290 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001516975290 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975290/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975290/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001516975290 Building ZINC001517065821 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065821' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065821 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001517065821 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065821/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065821 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/484 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cc(F)cc(Br)c1) `ZINC001517065821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001517065821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001517065821 none CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cc(F)cc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 8, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 8, 25, 25, 25, 17, 25, 25, 25, 11, 11, 11, 11, 11, 4, 7, 7, 25, 25, 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065821 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065821/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065821 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 485) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/485 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/485' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cc(F)cc(Br)c1) `ZINC001517065821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001517065821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001517065821 none CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cc(F)cc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 4, 7, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 7, 24, 24, 24, 14, 24, 24, 24, 10, 10, 10, 10, 10, 4, 8, 8, 24, 24, 24] 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065821 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001517065821 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065821/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065821/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065821 Building ZINC001517065821 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065821' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065821 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001517065821 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065821/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065821 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 484) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cc(F)cc(Br)c1) `ZINC001517065821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001517065821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001517065821 none CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cc(F)cc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 8, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 8, 25, 25, 25, 17, 25, 25, 25, 11, 11, 11, 11, 11, 4, 7, 7, 25, 25, 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065821 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065821/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065821 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 485) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cc(F)cc(Br)c1) `ZINC001517065821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001517065821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001517065821 none CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cc(F)cc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 4, 7, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 7, 24, 24, 24, 14, 24, 24, 24, 10, 10, 10, 10, 10, 4, 8, 8, 24, 24, 24] 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065821 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001517065821 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065821/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065821/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065821 Building ZINC001517065822 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065822' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065822 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001517065822 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065822/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065822 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/486 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cc(F)cc(Br)c1) `ZINC001517065822.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001517065822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001517065822 none CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cc(F)cc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 4, 7, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 7, 24, 24, 24, 15, 24, 24, 24, 10, 10, 10, 10, 10, 4, 8, 8, 24, 24, 24] 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065822 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065822/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065822 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 487) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/487 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/487' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cc(F)cc(Br)c1) `ZINC001517065822.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001517065822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001517065822 none CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cc(F)cc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 8, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 8, 25, 25, 25, 25, 25, 25, 25, 11, 11, 11, 11, 11, 4, 7, 7, 25, 25, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065822 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001517065822 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065822/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065822/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065822 Building ZINC001517065822 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065822' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065822 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001517065822 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065822/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065822 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 486) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cc(F)cc(Br)c1) `ZINC001517065822.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001517065822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001517065822 none CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cc(F)cc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 4, 7, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 7, 24, 24, 24, 15, 24, 24, 24, 10, 10, 10, 10, 10, 4, 8, 8, 24, 24, 24] 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065822 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065822/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065822 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 487) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cc(F)cc(Br)c1) `ZINC001517065822.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001517065822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001517065822 none CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cc(F)cc(Br)c1 NO_LONG_NAME dock atom types: ['C.3', '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', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 15, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 8, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 8, 25, 25, 25, 25, 25, 25, 25, 11, 11, 11, 11, 11, 4, 7, 7, 25, 25, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065822 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001517065822 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065822/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065822/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517065822 Building ZINC001517089137 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517089137' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517089137 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001517089137 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517089137/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517089137 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/488 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)cc1NC(=O)c1ccc(Cl)cc1F) `ZINC001517089137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001517089137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517089137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001517089137 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)cc1NC(=O)c1ccc(Cl)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 3, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 6, 6, 11, 11, 11, 17, 17, 17, 22, 22, 17, 22, 22, 22, 22, 21, 21, 21, 11, 11, 3, 6, 6, 2, 6, 6, 6, 6, 11, 17, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517089137 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517089137/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517089137 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 489) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/489 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/489' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)cc1NC(=O)c1ccc(Cl)cc1F) `ZINC001517089137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001517089137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517089137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001517089137 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)cc1NC(=O)c1ccc(Cl)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 6, 6, 12, 12, 12, 17, 17, 17, 21, 21, 17, 21, 21, 21, 21, 21, 21, 21, 12, 12, 3, 6, 6, 2, 6, 6, 6, 6, 12, 17, 21, 21, 21] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517089137 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001517089137 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517089137/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517089137/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517089137 Building ZINC001517089137 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517089137' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517089137 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001517089137 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517089137/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517089137 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 488) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)cc1NC(=O)c1ccc(Cl)cc1F) `ZINC001517089137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001517089137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517089137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001517089137 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)cc1NC(=O)c1ccc(Cl)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 3, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 6, 6, 11, 11, 11, 17, 17, 17, 22, 22, 17, 22, 22, 22, 22, 21, 21, 21, 11, 11, 3, 6, 6, 2, 6, 6, 6, 6, 11, 17, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517089137 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517089137/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517089137 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 489) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)cc1NC(=O)c1ccc(Cl)cc1F) `ZINC001517089137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001517089137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517089137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001517089137 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)cc1NC(=O)c1ccc(Cl)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 6, 6, 12, 12, 12, 17, 17, 17, 21, 21, 17, 21, 21, 21, 21, 21, 21, 21, 12, 12, 3, 6, 6, 2, 6, 6, 6, 6, 12, 17, 21, 21, 21] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517089137 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001517089137 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517089137/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517089137/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517089137 Building ZINC001517218444 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517218444' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517218444 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001517218444 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517218444/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517218444 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/490 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1)c1cccc(F)c1) `ZINC001517218444.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001517218444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517218444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001517218444 none O=C(Nc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1)c1cccc(F)c1 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.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', 'F', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 15, 1, 6, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 16, 50, 50, 50, 50, 50, 50, 16, 14, 14, 14, 6, 6, 1, 1, 1, 1, 14, 50, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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/12845/xbi-8058088.35/working/building/ZINC001517218444 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517218444/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517218444 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 491) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/491 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/491' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1)c1cccc(F)c1) `ZINC001517218444.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001517218444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517218444/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001517218444 none O=C(Nc1cccc(CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1)c1cccc(F)c1 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.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', 'F', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 15, 1, 6, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 15, 15, 15, 15, 15, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 15, 17, 50, 50, 50, 50, 50, 50, 17, 15, 15, 15, 7, 7, 2, 2, 2, 2, 15, 50, 50, 50, 50] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517218444 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001517218444 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517218444/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517218444/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517218444 Building ZINC001517218444 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517218444' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517218444 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001517218444 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517218444/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517218444 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 490) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1)c1cccc(F)c1) `ZINC001517218444.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001517218444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517218444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001517218444 none O=C(Nc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1)c1cccc(F)c1 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.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', 'F', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 15, 1, 6, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 16, 50, 50, 50, 50, 50, 50, 16, 14, 14, 14, 6, 6, 1, 1, 1, 1, 14, 50, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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/12845/xbi-8058088.35/working/building/ZINC001517218444 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517218444/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517218444 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 491) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1cccc(CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1)c1cccc(F)c1) `ZINC001517218444.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001517218444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517218444/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001517218444 none O=C(Nc1cccc(CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c1)c1cccc(F)c1 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.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', 'F', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 15, 1, 6, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 15, 15, 15, 15, 15, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 15, 17, 50, 50, 50, 50, 50, 50, 17, 15, 15, 15, 7, 7, 2, 2, 2, 2, 15, 50, 50, 50, 50] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517218444 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001517218444 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517218444/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517218444/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517218444 Building ZINC001517473144 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517473144' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517473144 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001517473144 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517473144/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517473144 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/492 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)c(OCc2ccccc2)c1) `ZINC001517473144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001517473144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517473144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001517473144 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)c(OCc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 3, 3, 2, 3, 5, 3, 3, 3, 3, 3, 6, 11, 17, 17, 13, 17, 17, 3, 5, 5, 5, 3, 3, 2, 3, 3, 5, 5, 5, 3, 11, 11, 17, 17, 17, 17, 17, 3] 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517473144 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517473144/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517473144 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 493) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/493 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/493' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)c(OCc2ccccc2)c1) `ZINC001517473144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001517473144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517473144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001517473144 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)c(OCc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 3, 3, 2, 3, 5, 3, 3, 3, 3, 3, 7, 12, 17, 17, 14, 17, 17, 3, 5, 5, 5, 3, 3, 2, 3, 3, 5, 5, 5, 3, 12, 12, 17, 17, 17, 17, 17, 3] 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517473144 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001517473144 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517473144/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517473144/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517473144 Building ZINC001517473144 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517473144' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517473144 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001517473144 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517473144/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517473144 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 492) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)c(OCc2ccccc2)c1) `ZINC001517473144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001517473144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517473144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001517473144 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)c(OCc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 3, 3, 2, 3, 5, 3, 3, 3, 3, 3, 6, 11, 17, 17, 13, 17, 17, 3, 5, 5, 5, 3, 3, 2, 3, 3, 5, 5, 5, 3, 11, 11, 17, 17, 17, 17, 17, 3] 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517473144 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517473144/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517473144 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 493) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)c(OCc2ccccc2)c1) `ZINC001517473144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001517473144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517473144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC001517473144 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)c(OCc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 3, 3, 2, 3, 5, 3, 3, 3, 3, 3, 7, 12, 17, 17, 14, 17, 17, 3, 5, 5, 5, 3, 3, 2, 3, 3, 5, 5, 5, 3, 12, 12, 17, 17, 17, 17, 17, 3] 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517473144 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001517473144 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517473144/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517473144/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517473144 Building ZINC001517566756 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517566756' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517566756 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001517566756 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517566756/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517566756 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/494 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccc(COc2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001517566756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001517566756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517566756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001517566756 none O=C(NCc1cccc(COc2ccccc2)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', 'C.3', 'O.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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 5, 12, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 28, 28, 16, 28, 28, 50, 50, 50, 50, 50, 50, 50, 25, 1, 1, 1, 3, 3, 3, 3, 3, 2, 10, 10, 28, 28, 17, 50, 50, 50, 50, 50, 50, 50, 28, 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: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517566756 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517566756/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517566756 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 495) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/495 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/495' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cccc(COc2ccccc2)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001517566756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001517566756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517566756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001517566756 none O=C(NCc1cccc(COc2ccccc2)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', 'C.3', 'O.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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 5, 12, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 25, 1, 1, 1, 3, 3, 3, 3, 3, 2, 10, 10, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 28, 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: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517566756 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001517566756 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517566756/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517566756/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517566756 Building ZINC001517566756 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517566756' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517566756 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001517566756 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517566756/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517566756 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 494) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NCc1cccc(COc2ccccc2)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001517566756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001517566756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517566756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001517566756 none O=C(NCc1cccc(COc2ccccc2)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', 'C.3', 'O.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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 5, 12, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 28, 28, 16, 28, 28, 50, 50, 50, 50, 50, 50, 50, 25, 1, 1, 1, 3, 3, 3, 3, 3, 2, 10, 10, 28, 28, 17, 50, 50, 50, 50, 50, 50, 50, 28, 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: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517566756 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517566756/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517566756 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 495) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NCc1cccc(COc2ccccc2)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001517566756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001517566756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517566756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001517566756 none O=C(NCc1cccc(COc2ccccc2)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', 'C.3', 'O.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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 5, 12, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 25, 1, 1, 1, 3, 3, 3, 3, 3, 2, 10, 10, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 28, 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: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517566756 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001517566756 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517566756/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517566756/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517566756 Building ZINC001517589911 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517589911' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517589911 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001517589911 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517589911/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517589911 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/496 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCCCC2)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001517589911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001517589911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517589911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001517589911 none O=C(Nc1ccc(N2CCCCC2)c(Cl)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', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 16, 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, 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, 12, 12, 9, 20, 37, 37, 37, 37, 37, 12, 12, 12, 1, 1, 1, 9, 9, 9, 9, 9, 3, 12, 12, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 12, 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: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517589911 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517589911/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517589911 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 497) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/497 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/497' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCCCC2)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001517589911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001517589911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517589911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001517589911 none O=C(Nc1ccc(N2CCCCC2)c(Cl)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', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 16, 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, 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, 11, 11, 19, 36, 36, 36, 36, 36, 11, 11, 11, 1, 1, 1, 10, 10, 10, 10, 10, 2, 11, 11, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 11, 10, 10] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517589911 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001517589911 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517589911/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517589911/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517589911 Building ZINC001517589911 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517589911' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517589911 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001517589911 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517589911/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517589911 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 496) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(Nc1ccc(N2CCCCC2)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001517589911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001517589911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517589911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001517589911 none O=C(Nc1ccc(N2CCCCC2)c(Cl)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', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 16, 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, 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, 12, 12, 9, 20, 37, 37, 37, 37, 37, 12, 12, 12, 1, 1, 1, 9, 9, 9, 9, 9, 3, 12, 12, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 12, 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: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517589911 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517589911/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517589911 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 497) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(Nc1ccc(N2CCCCC2)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001517589911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001517589911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517589911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001517589911 none O=C(Nc1ccc(N2CCCCC2)c(Cl)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', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 16, 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, 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, 11, 11, 19, 36, 36, 36, 36, 36, 11, 11, 11, 1, 1, 1, 10, 10, 10, 10, 10, 2, 11, 11, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 11, 10, 10] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517589911 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001517589911 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517589911/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517589911/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517589911 Building ZINC001517592463 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592463' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592463 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001517592463 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592463/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592463 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/498 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2nc(c3ccc(Br)cc3)cs2)cc1) `ZINC001517592463.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001517592463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001517592463 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2nc(c3ccc(Br)cc3)cs2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 34, 34, 34, 50, 50, 34, 50, 50, 50, 34, 34, 2, 2, 2, 2, 2, 2, 2, 3, 6, 6, 6, 50, 50, 50, 50, 34, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592463 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592463/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592463 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 499) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/499 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/499' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2nc(c3ccc(Br)cc3)cs2)cc1) `ZINC001517592463.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001517592463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592463/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001517592463 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2nc(c3ccc(Br)cc3)cs2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 31, 31, 31, 50, 50, 31, 48, 50, 50, 31, 31, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 50, 50, 50, 50, 31, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592463 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001517592463 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592463/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592463/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592463 Building ZINC001517592463 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592463' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592463 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001517592463 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592463/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592463 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 498) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2nc(c3ccc(Br)cc3)cs2)cc1) `ZINC001517592463.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001517592463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001517592463 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2nc(c3ccc(Br)cc3)cs2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 34, 34, 34, 50, 50, 34, 50, 50, 50, 34, 34, 2, 2, 2, 2, 2, 2, 2, 3, 6, 6, 6, 50, 50, 50, 50, 34, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592463 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592463/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592463 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 499) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2nc(c3ccc(Br)cc3)cs2)cc1) `ZINC001517592463.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001517592463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592463/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001517592463 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2nc(c3ccc(Br)cc3)cs2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 31, 31, 31, 50, 50, 31, 48, 50, 50, 31, 31, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 50, 50, 50, 50, 31, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592463 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001517592463 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592463/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592463/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592463 Building ZINC001517592503 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592503' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592503 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001517592503 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592503/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592503 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/500 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2nc(c3ccc(Br)cc3)cs2)cc1) `ZINC001517592503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001517592503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001517592503 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2nc(c3ccc(Br)cc3)cs2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 31, 31, 31, 50, 50, 31, 31, 50, 50, 31, 31, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 50, 50, 50, 50, 31, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592503 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592503/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592503 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 501) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/501 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/501' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2nc(c3ccc(Br)cc3)cs2)cc1) `ZINC001517592503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001517592503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001517592503 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2nc(c3ccc(Br)cc3)cs2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 34, 34, 34, 50, 50, 34, 34, 50, 50, 34, 34, 2, 2, 2, 2, 2, 2, 2, 3, 6, 6, 6, 50, 50, 50, 50, 34, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592503 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001517592503 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592503/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592503/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592503 Building ZINC001517592503 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592503' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592503 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001517592503 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592503/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592503 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 500) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2nc(c3ccc(Br)cc3)cs2)cc1) `ZINC001517592503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001517592503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001517592503 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2nc(c3ccc(Br)cc3)cs2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 31, 31, 31, 50, 50, 31, 31, 50, 50, 31, 31, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 50, 50, 50, 50, 31, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592503 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592503/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592503 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 501) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2nc(c3ccc(Br)cc3)cs2)cc1) `ZINC001517592503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001517592503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001517592503 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2nc(c3ccc(Br)cc3)cs2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 34, 34, 34, 50, 50, 34, 34, 50, 50, 34, 34, 2, 2, 2, 2, 2, 2, 2, 3, 6, 6, 6, 50, 50, 50, 50, 34, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592503 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001517592503 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592503/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592503/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517592503 Building ZINC001517618331 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618331' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618331 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001517618331 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618331/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618331 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/502 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](Cc1ccccn1)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001517618331.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001517618331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001517618331 none O=C(N[C@H](Cc1ccccn1)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 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, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 21, 21, 21, 21, 21, 8, 10, 10, 10, 10, 10, 10, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 15, 15, 21, 21, 21, 21, 10, 10, 10, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 90 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618331 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618331/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618331 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 503) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/503 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/503' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](Cc1ccccn1)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001517618331.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001517618331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001517618331 none O=C(N[C@H](Cc1ccccn1)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 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, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 20, 20, 20, 20, 20, 7, 11, 11, 7, 8, 11, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 16, 16, 20, 20, 20, 20, 11, 11, 11, 11, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 104 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618331 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001517618331 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618331/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618331/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618331 Building ZINC001517618331 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618331' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618331 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001517618331 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618331/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618331 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 502) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/502: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](Cc1ccccn1)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001517618331.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001517618331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001517618331 none O=C(N[C@H](Cc1ccccn1)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 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, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 21, 21, 21, 21, 21, 8, 10, 10, 10, 10, 10, 10, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 15, 15, 21, 21, 21, 21, 10, 10, 10, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 90 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618331 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618331/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618331 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 503) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/503: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](Cc1ccccn1)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001517618331.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001517618331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001517618331 none O=C(N[C@H](Cc1ccccn1)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 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, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 20, 20, 20, 20, 20, 7, 11, 11, 7, 8, 11, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 16, 16, 20, 20, 20, 20, 11, 11, 11, 11, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 104 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618331 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001517618331 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618331/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618331/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618331 Building ZINC001517618339 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618339' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618339 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001517618339 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618339/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618339 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/504 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](Cc1ccccn1)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001517618339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001517618339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001517618339 none O=C(N[C@@H](Cc1ccccn1)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 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, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 19, 19, 19, 19, 19, 7, 11, 11, 11, 11, 11, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 14, 14, 19, 19, 19, 19, 11, 11, 11, 11, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 86 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618339 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618339/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618339 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 505) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/505 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/505' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](Cc1ccccn1)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001517618339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001517618339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001517618339 none O=C(N[C@@H](Cc1ccccn1)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 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, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 21, 21, 21, 21, 21, 8, 10, 10, 10, 10, 10, 10, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 15, 15, 21, 21, 21, 21, 10, 10, 10, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 90 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618339 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001517618339 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618339/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618339/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618339 Building ZINC001517618339 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618339' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618339 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001517618339 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618339/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618339 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 504) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N[C@@H](Cc1ccccn1)c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001517618339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001517618339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001517618339 none O=C(N[C@@H](Cc1ccccn1)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 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, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 19, 19, 19, 19, 19, 7, 11, 11, 11, 11, 11, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 14, 14, 19, 19, 19, 19, 11, 11, 11, 11, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 86 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618339 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618339/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618339 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 505) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N[C@@H](Cc1ccccn1)c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001517618339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001517618339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001517618339 none O=C(N[C@@H](Cc1ccccn1)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 1, 8, 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, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 21, 21, 21, 21, 21, 8, 10, 10, 10, 10, 10, 10, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 15, 15, 21, 21, 21, 21, 10, 10, 10, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 90 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618339 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001517618339 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618339/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618339/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517618339 Building ZINC001517626175 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517626175' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517626175 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001517626175 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517626175/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517626175 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/506 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2cccc(Cl)c2)CCOCC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001517626175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001517626175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517626175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001517626175 none O=C(NCC1(c2cccc(Cl)c2)CCOCC1)[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', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 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, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 29, 48, 48, 48, 48, 48, 48, 29, 29, 29, 29, 29, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 11, 11, 48, 48, 48, 48, 29, 29, 29, 29, 29, 29, 29, 29, 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, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 127 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517626175 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517626175/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517626175 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 507) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/507 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/507' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2cccc(Cl)c2)CCOCC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001517626175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001517626175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517626175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001517626175 none O=C(NCC1(c2cccc(Cl)c2)CCOCC1)[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', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 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, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 25, 46, 46, 46, 46, 46, 46, 25, 25, 25, 25, 25, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 9, 9, 46, 46, 46, 46, 25, 25, 25, 25, 25, 25, 25, 25, 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, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 115 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517626175 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001517626175 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517626175/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517626175/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517626175 Building ZINC001517626175 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517626175' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517626175 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001517626175 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517626175/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517626175 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 506) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NCC1(c2cccc(Cl)c2)CCOCC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001517626175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001517626175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517626175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001517626175 none O=C(NCC1(c2cccc(Cl)c2)CCOCC1)[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', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 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, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 29, 48, 48, 48, 48, 48, 48, 29, 29, 29, 29, 29, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 11, 11, 48, 48, 48, 48, 29, 29, 29, 29, 29, 29, 29, 29, 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, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 127 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517626175 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517626175/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517626175 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 507) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NCC1(c2cccc(Cl)c2)CCOCC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001517626175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001517626175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517626175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001517626175 none O=C(NCC1(c2cccc(Cl)c2)CCOCC1)[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', 'Cl', 'C.ar', 'C.3', 'C.3', 'O.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 12, 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, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 25, 46, 46, 46, 46, 46, 46, 25, 25, 25, 25, 25, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 9, 9, 46, 46, 46, 46, 25, 25, 25, 25, 25, 25, 25, 25, 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, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 115 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517626175 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001517626175 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517626175/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517626175/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517626175 Building ZINC001517646878 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517646878' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517646878 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001517646878 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517646878/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517646878 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/508 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(N(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C2CC2)CC1) `ZINC001517646878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001517646878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517646878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001517646878 none CC(C)(C)OC(=O)N1CCC(N(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C2CC2)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', '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, 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, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 13, 25, 13, 13, 12, 7, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 10, 10, 13, 13, 45, 45, 45, 45, 45, 45, 45, 45, 45, 13, 13, 13, 13, 13, 3, 3, 3, 10, 10, 10, 10, 10, 13, 13, 13, 13] 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]) total number of confs: 137 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517646878 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517646878/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517646878 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 509) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/509 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/509' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(N(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C2CC2)CC1) `ZINC001517646878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001517646878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) Traceback (most recent call last): File "/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/amsol/process_amsol_mol2.py", line 476, in main() File "/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/amsol/process_amsol_mol2.py", line 458, in main diff_amsol71_files(atom_list_wat, tot_wat, atom_list_hex, tot_hex, name_wat, numat_wat, outputprefix) File "/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/amsol/process_amsol_mol2.py", line 273, in diff_amsol71_files Sigmahex[i] = float(atom_listhex[i][5]) # Sigma (kcal/Ang**2) ValueError: could not convert string to float: ******* Solvation calculation failed Skipping ZINC001517646878 1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517646878 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 `1' -> `1.failed' Finished preparing ZINC001517646878 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Found failed protomers Marking ZINC001517646878 as failed mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/failed' `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517646878' -> `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878' Building ZINC001517646878 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517646878' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517646878 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001517646878 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517646878/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517646878 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 508) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)OC(=O)N1CCC(N(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C2CC2)CC1) `ZINC001517646878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001517646878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517646878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001517646878 none CC(C)(C)OC(=O)N1CCC(N(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C2CC2)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', '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, 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, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 13, 25, 13, 13, 12, 7, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 10, 10, 13, 13, 45, 45, 45, 45, 45, 45, 45, 45, 45, 13, 13, 13, 13, 13, 3, 3, 3, 10, 10, 10, 10, 10, 13, 13, 13, 13] 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]) total number of confs: 137 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517646878 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517646878/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517646878 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 509) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)OC(=O)N1CCC(N(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C2CC2)CC1) `ZINC001517646878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001517646878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) Traceback (most recent call last): File "/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/amsol/process_amsol_mol2.py", line 476, in main() File "/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/amsol/process_amsol_mol2.py", line 458, in main diff_amsol71_files(atom_list_wat, tot_wat, atom_list_hex, tot_hex, name_wat, numat_wat, outputprefix) File "/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/amsol/process_amsol_mol2.py", line 273, in diff_amsol71_files Sigmahex[i] = float(atom_listhex[i][5]) # Sigma (kcal/Ang**2) ValueError: could not convert string to float: ******* Solvation calculation failed Skipping ZINC001517646878 1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517646878 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 `1' -> `1.failed' Finished preparing ZINC001517646878 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Found failed protomers Marking ZINC001517646878 as failed `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517646878' -> `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878' Building ZINC001517714975 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517714975' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517714975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001517714975 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517714975/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517714975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/510 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(F)cc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccn1) `ZINC001517714975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001517714975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517714975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001517714975 none O=C(Nc1ccc(F)cc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccn1 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', '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', 'N.ar', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 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] 0 hydrogens 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, 35, 18, 18, 18, 18, 18, 18, 18, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 35, 42, 42, 42, 42, 42, 36, 18, 18, 18, 4, 3, 1, 3, 42, 42, 42, 42] 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517714975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517714975/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517714975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 511) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/511 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/511' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(F)cc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccn1) `ZINC001517714975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001517714975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517714975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001517714975 none O=C(Nc1ccc(F)cc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccn1 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', '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', 'N.ar', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 34, 17, 17, 17, 11, 17, 17, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 34, 42, 42, 42, 42, 42, 35, 17, 11, 17, 4, 3, 1, 3, 42, 42, 42, 42] 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]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517714975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001517714975 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517714975/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517714975/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517714975 Building ZINC001517714975 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517714975' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517714975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001517714975 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517714975/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517714975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 510) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/510: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(F)cc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccn1) `ZINC001517714975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001517714975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517714975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001517714975 none O=C(Nc1ccc(F)cc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccn1 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', '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', 'N.ar', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 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] 0 hydrogens 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, 35, 18, 18, 18, 18, 18, 18, 18, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 35, 42, 42, 42, 42, 42, 36, 18, 18, 18, 4, 3, 1, 3, 42, 42, 42, 42] 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517714975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517714975/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517714975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 511) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/511: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(F)cc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccn1) `ZINC001517714975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001517714975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517714975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001517714975 none O=C(Nc1ccc(F)cc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccccn1 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', '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', 'N.ar', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 8, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 34, 17, 17, 17, 11, 17, 17, 17, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 34, 42, 42, 42, 42, 42, 35, 17, 11, 17, 4, 3, 1, 3, 42, 42, 42, 42] 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]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517714975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001517714975 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517714975/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517714975/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517714975 Building ZINC001517915643 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517915643' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517915643 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001517915643 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517915643/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517915643 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/512 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCOc1cc(C)ccc1CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001517915643.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001517915643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517915643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001517915643 none CCCCCOc1cc(C)ccc1CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 43, 30, 12, 8, 8, 8, 8, 8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 46, 46, 46, 46, 46, 46, 46, 46, 46, 30, 30, 8, 8, 8, 8, 8, 8, 3, 3, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [19, 13, 14, 15, 16, 17, 18, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517915643 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517915643/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517915643 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 513) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/513 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/513' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCOc1cc(C)ccc1CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001517915643.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001517915643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517915643/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001517915643 none CCCCCOc1cc(C)ccc1CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 42, 30, 13, 8, 8, 8, 8, 8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 45, 45, 45, 45, 45, 45, 45, 45, 45, 30, 30, 8, 8, 8, 8, 8, 8, 3, 3, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [19, 13, 14, 15, 16, 17, 18, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517915643 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001517915643 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517915643/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517915643/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517915643 Building ZINC001517915643 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517915643' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517915643 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001517915643 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517915643/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517915643 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 512) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCCCCOc1cc(C)ccc1CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001517915643.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001517915643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517915643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001517915643 none CCCCCOc1cc(C)ccc1CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 43, 30, 12, 8, 8, 8, 8, 8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 46, 46, 46, 46, 46, 46, 46, 46, 46, 30, 30, 8, 8, 8, 8, 8, 8, 3, 3, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [19, 13, 14, 15, 16, 17, 18, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517915643 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517915643/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517915643 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 513) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCCCCOc1cc(C)ccc1CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001517915643.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001517915643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517915643/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001517915643 none CCCCCOc1cc(C)ccc1CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 45, 42, 30, 13, 8, 8, 8, 8, 8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 45, 45, 45, 45, 45, 45, 45, 45, 45, 30, 30, 8, 8, 8, 8, 8, 8, 3, 3, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [19, 13, 14, 15, 16, 17, 18, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517915643 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001517915643 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517915643/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517915643/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517915643 Building ZINC001517919963 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517919963' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517919963 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001517919963 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517919963/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517919963 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/514 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)C)c(OC)c1) `ZINC001517919963.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001517919963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517919963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001517919963 none COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)C)c(OC)c1 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.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 1, 12, 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, 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] 0 hydrogens 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, 12, 12, 12, 12, 9, 6, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 6, 12, 12, 12, 12, 12, 20, 12, 21, 21, 21, 12, 12, 9, 9, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 20, 20, 20, 12] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 113 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517919963 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517919963/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517919963 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 515) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/515 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/515' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)C)c(OC)c1) `ZINC001517919963.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001517919963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517919963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001517919963 none COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)C)c(OC)c1 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.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 1, 12, 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, 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] 0 hydrogens 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, 13, 10, 13, 13, 10, 6, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 11, 11, 11, 13, 13, 22, 13, 23, 23, 23, 13, 13, 10, 10, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 128 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517919963 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001517919963 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517919963/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517919963/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517919963 Building ZINC001517919963 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517919963' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517919963 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001517919963 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517919963/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517919963 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 514) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)C)c(OC)c1) `ZINC001517919963.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001517919963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517919963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001517919963 none COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)C)c(OC)c1 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.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 1, 12, 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, 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] 0 hydrogens 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, 12, 12, 12, 12, 9, 6, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 6, 12, 12, 12, 12, 12, 20, 12, 21, 21, 21, 12, 12, 9, 9, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 20, 20, 20, 12] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 113 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517919963 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517919963/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517919963 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 515) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)C)c(OC)c1) `ZINC001517919963.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001517919963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517919963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001517919963 none COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C(C)(C)C)c(OC)c1 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.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 1, 12, 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, 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] 0 hydrogens 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, 13, 10, 13, 13, 10, 6, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 11, 11, 11, 13, 13, 22, 13, 23, 23, 23, 13, 13, 10, 10, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 128 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517919963 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001517919963 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517919963/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517919963/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001517919963 Building ZINC001518074071 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518074071' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518074071 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001518074071 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518074071/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518074071 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/516 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2cccc(Br)c2n1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001518074071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001518074071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518074071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001518074071 none O=C(Nc1ccc2cccc(Br)c2n1)[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.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 8, 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, 3, 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: [11, 1, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 12, 12, 12, 12, 12, 11, 21, 21, 21, 21, 21, 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: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518074071 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518074071/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518074071 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 517) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/517 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/517' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2cccc(Br)c2n1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001518074071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001518074071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518074071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001518074071 none O=C(Nc1ccc2cccc(Br)c2n1)[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.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 8, 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, 3, 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: [11, 1, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 12, 12, 12, 12, 12, 11, 21, 21, 21, 21, 21, 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: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518074071 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001518074071 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518074071/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518074071/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518074071 Building ZINC001518074071 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518074071' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518074071 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001518074071 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518074071/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518074071 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 516) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/516: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2cccc(Br)c2n1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001518074071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001518074071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518074071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001518074071 none O=C(Nc1ccc2cccc(Br)c2n1)[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.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 8, 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, 3, 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: [11, 1, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 12, 12, 12, 12, 12, 11, 21, 21, 21, 21, 21, 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: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518074071 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518074071/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518074071 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 517) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/517: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2cccc(Br)c2n1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001518074071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001518074071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518074071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001518074071 none O=C(Nc1ccc2cccc(Br)c2n1)[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.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 8, 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, 3, 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: [11, 1, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 12, 12, 12, 12, 12, 11, 21, 21, 21, 21, 21, 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: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518074071 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001518074071 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518074071/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518074071/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518074071 Building ZINC001518219936 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219936' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219936 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001518219936 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219936/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219936 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/518 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Cl)ccc2OC[C@@H]2CCCCO2)cc1Cl) `ZINC001518219936.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001518219936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001518219936 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Cl)ccc2OC[C@@H]2CCCCO2)cc1Cl NO_LONG_NAME dock atom 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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 4, 12, 25, 27, 27, 27, 27, 27, 27, 4, 4, 4, 8, 8, 8, 4, 4, 2, 4, 4, 4, 22, 22, 27, 27, 27, 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219936 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219936/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219936 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 519) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/519 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/519' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Cl)ccc2OC[C@@H]2CCCCO2)cc1Cl) `ZINC001518219936.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001518219936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001518219936 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Cl)ccc2OC[C@@H]2CCCCO2)cc1Cl NO_LONG_NAME dock atom 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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 2, 5, 5, 5, 14, 27, 29, 29, 29, 29, 29, 29, 4, 4, 4, 8, 8, 8, 4, 4, 2, 5, 4, 5, 25, 25, 29, 29, 29, 29, 29, 29, 29, 29, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219936 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001518219936 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219936/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219936/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219936 Building ZINC001518219936 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219936' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219936 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001518219936 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219936/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219936 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 518) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Cl)ccc2OC[C@@H]2CCCCO2)cc1Cl) `ZINC001518219936.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001518219936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001518219936 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Cl)ccc2OC[C@@H]2CCCCO2)cc1Cl NO_LONG_NAME dock atom 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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 4, 4, 4, 4, 12, 25, 27, 27, 27, 27, 27, 27, 4, 4, 4, 8, 8, 8, 4, 4, 2, 4, 4, 4, 22, 22, 27, 27, 27, 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219936 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219936/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219936 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 519) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Cl)ccc2OC[C@@H]2CCCCO2)cc1Cl) `ZINC001518219936.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001518219936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001518219936 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Cl)ccc2OC[C@@H]2CCCCO2)cc1Cl NO_LONG_NAME dock atom 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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 2, 5, 5, 5, 14, 27, 29, 29, 29, 29, 29, 29, 4, 4, 4, 8, 8, 8, 4, 4, 2, 5, 4, 5, 25, 25, 29, 29, 29, 29, 29, 29, 29, 29, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219936 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001518219936 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219936/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219936/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219936 Building ZINC001518219937 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219937' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219937 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001518219937 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219937/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219937 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/520 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Cl)ccc2OC[C@H]2CCCCO2)cc1Cl) `ZINC001518219937.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001518219937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001518219937 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Cl)ccc2OC[C@H]2CCCCO2)cc1Cl NO_LONG_NAME dock atom 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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 2, 5, 5, 5, 15, 27, 29, 29, 29, 29, 29, 29, 4, 4, 4, 8, 8, 8, 4, 4, 2, 5, 4, 5, 25, 25, 29, 29, 29, 29, 29, 29, 29, 29, 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219937 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219937/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219937 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 521) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/521 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/521' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Cl)ccc2OC[C@H]2CCCCO2)cc1Cl) `ZINC001518219937.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001518219937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219937/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001518219937 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Cl)ccc2OC[C@H]2CCCCO2)cc1Cl NO_LONG_NAME dock atom 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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 2, 4, 4, 4, 12, 24, 26, 26, 26, 26, 26, 26, 4, 4, 4, 8, 8, 8, 4, 4, 2, 4, 4, 4, 21, 21, 26, 26, 26, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219937 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001518219937 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219937/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219937/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219937 Building ZINC001518219937 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219937' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219937 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001518219937 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219937/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219937 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 520) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Cl)ccc2OC[C@H]2CCCCO2)cc1Cl) `ZINC001518219937.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001518219937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001518219937 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Cl)ccc2OC[C@H]2CCCCO2)cc1Cl NO_LONG_NAME dock atom 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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 2, 5, 5, 5, 15, 27, 29, 29, 29, 29, 29, 29, 4, 4, 4, 8, 8, 8, 4, 4, 2, 5, 4, 5, 25, 25, 29, 29, 29, 29, 29, 29, 29, 29, 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219937 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219937/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219937 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 521) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Cl)ccc2OC[C@H]2CCCCO2)cc1Cl) `ZINC001518219937.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001518219937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219937/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001518219937 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Cl)ccc2OC[C@H]2CCCCO2)cc1Cl NO_LONG_NAME dock atom 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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 5, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 2, 4, 4, 4, 12, 24, 26, 26, 26, 26, 26, 26, 4, 4, 4, 8, 8, 8, 4, 4, 2, 4, 4, 4, 21, 21, 26, 26, 26, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219937 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001518219937 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219937/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219937/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518219937 Building ZINC001518242658 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518242658' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518242658 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001518242658 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518242658/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518242658 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/522 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/522' -> `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)cc2)cc1OCC) `ZINC001518242658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001518242658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518242658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001518242658 none CCOc1cc(Br)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 31, 8, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 8, 8, 30, 36, 42, 42, 42, 42, 42, 8, 4, 3, 3, 3, 3, 8, 36, 36, 36, 36, 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]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518242658 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518242658/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518242658 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 523) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/523 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/523' -> `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)cc2)cc1OCC) `ZINC001518242658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001518242658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518242658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001518242658 none CCOc1cc(Br)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 31, 8, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 8, 8, 8, 30, 36, 42, 42, 42, 42, 42, 8, 4, 3, 3, 3, 3, 8, 36, 36, 36, 36, 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]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518242658 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001518242658 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518242658/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518242658/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518242658 Building ZINC001518242658 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518242658' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518242658 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001518242658 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518242658/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518242658 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 522) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOc1cc(Br)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1OCC) `ZINC001518242658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001518242658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518242658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001518242658 none CCOc1cc(Br)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 31, 8, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 8, 8, 30, 36, 42, 42, 42, 42, 42, 8, 4, 3, 3, 3, 3, 8, 36, 36, 36, 36, 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]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518242658 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518242658/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518242658 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 523) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOc1cc(Br)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1OCC) `ZINC001518242658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001518242658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518242658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001518242658 none CCOc1cc(Br)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 31, 8, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 8, 8, 8, 30, 36, 42, 42, 42, 42, 42, 8, 4, 3, 3, 3, 3, 8, 36, 36, 36, 36, 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]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518242658 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001518242658 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518242658/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518242658/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518242658 Building ZINC001518425202 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518425202' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518425202 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001518425202 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518425202/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518425202 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/524 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/524' -> `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])c2ccc(Cl)s2)CC1) `ZINC001518425202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001518425202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518425202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001518425202 none CC1(c2cccc(Br)c2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)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.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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 32, 32, 32, 32, 32, 32, 10, 10, 6, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 32, 32, 32, 32, 10, 10, 10, 10, 3, 3, 10, 10, 10, 10] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518425202 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518425202/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518425202 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 525) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/525 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/525' -> `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])c2ccc(Cl)s2)CC1) `ZINC001518425202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001518425202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518425202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001518425202 none CC1(c2cccc(Br)c2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)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.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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 30, 30, 30, 30, 30, 30, 10, 10, 6, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 30, 30, 30, 30, 10, 10, 10, 10, 3, 3, 10, 10, 10, 10] 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]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518425202 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001518425202 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518425202/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518425202/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518425202 Building ZINC001518425202 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518425202' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518425202 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001518425202 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518425202/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518425202 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 524) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC1(c2cccc(Br)c2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001518425202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001518425202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518425202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001518425202 none CC1(c2cccc(Br)c2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)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.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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 32, 32, 32, 32, 32, 32, 10, 10, 6, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 32, 32, 32, 32, 10, 10, 10, 10, 3, 3, 10, 10, 10, 10] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518425202 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518425202/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518425202 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 525) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC1(c2cccc(Br)c2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001518425202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001518425202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518425202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001518425202 none CC1(c2cccc(Br)c2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)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.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'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 30, 30, 30, 30, 30, 30, 10, 10, 6, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 30, 30, 30, 30, 10, 10, 10, 10, 3, 3, 10, 10, 10, 10] 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]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518425202 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001518425202 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518425202/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518425202/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518425202 Building ZINC001518431219 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518431219' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518431219 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001518431219 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518431219/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518431219 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/526 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)COC(=O)Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001518431219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001518431219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518431219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001518431219 none CC(C)COC(=O)Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 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, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 35, 13, 13, 13, 13, 9, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 9, 35, 35, 35, 35, 35, 35, 35, 29, 29, 13, 9, 9, 9, 3, 6, 6, 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518431219 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518431219/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518431219 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 527) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/527 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/527' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)COC(=O)Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001518431219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001518431219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518431219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001518431219 none CC(C)COC(=O)Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 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, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 34, 13, 13, 13, 13, 9, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 9, 34, 34, 34, 34, 34, 34, 34, 26, 26, 13, 9, 9, 9, 3, 7, 7, 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]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518431219 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001518431219 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518431219/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518431219/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518431219 Building ZINC001518431219 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518431219' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518431219 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001518431219 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518431219/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518431219 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 526) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)COC(=O)Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001518431219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001518431219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518431219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001518431219 none CC(C)COC(=O)Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 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, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 35, 13, 13, 13, 13, 9, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 9, 35, 35, 35, 35, 35, 35, 35, 29, 29, 13, 9, 9, 9, 3, 6, 6, 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518431219 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518431219/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518431219 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 527) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)COC(=O)Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001518431219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001518431219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518431219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001518431219 none CC(C)COC(=O)Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 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, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 34, 13, 13, 13, 13, 9, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 9, 34, 34, 34, 34, 34, 34, 34, 26, 26, 13, 9, 9, 9, 3, 7, 7, 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]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518431219 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001518431219 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518431219/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518431219/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518431219 Building ZINC001518484903 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518484903' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518484903 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001518484903 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518484903/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518484903 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/528 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/528' -> `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)c1cccc(Cl)c1F) `ZINC001518484903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001518484903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518484903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001518484903 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)c1cccc(Cl)c1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'Cl', '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, 5, 5, 5, 1, 1, 1, 1, 1, 16, 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] 0 hydrogens need rotated 50 conformations in 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, 12, 32, 34, 36, 43, 43, 43, 43, 43, 43, 43, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 3, 12, 12, 36, 36, 36, 36, 36, 36, 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: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518484903 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518484903/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518484903 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 529) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/529 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/529' -> `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)c1cccc(Cl)c1F) `ZINC001518484903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001518484903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518484903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001518484903 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(C)(C)c1cccc(Cl)c1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'Cl', '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, 5, 5, 5, 1, 1, 1, 1, 1, 16, 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] 0 hydrogens need rotated 50 conformations in 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, 13, 33, 31, 35, 42, 42, 42, 42, 42, 42, 42, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 13, 13, 35, 35, 35, 35, 35, 35, 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: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518484903 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001518484903 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518484903/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518484903/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518484903 Building ZINC001518484903 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518484903' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518484903 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001518484903 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518484903/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518484903 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 528) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/528: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)c1cccc(Cl)c1F) `ZINC001518484903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001518484903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518484903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001518484903 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)c1cccc(Cl)c1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'Cl', '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, 5, 5, 5, 1, 1, 1, 1, 1, 16, 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] 0 hydrogens need rotated 50 conformations in 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, 12, 32, 34, 36, 43, 43, 43, 43, 43, 43, 43, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 3, 12, 12, 36, 36, 36, 36, 36, 36, 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: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518484903 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518484903/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518484903 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 529) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/529: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(C)(C)c1cccc(Cl)c1F) `ZINC001518484903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001518484903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518484903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001518484903 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(C)(C)c1cccc(Cl)c1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'Cl', '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, 5, 5, 5, 1, 1, 1, 1, 1, 16, 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] 0 hydrogens need rotated 50 conformations in 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, 13, 33, 31, 35, 42, 42, 42, 42, 42, 42, 42, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 13, 13, 35, 35, 35, 35, 35, 35, 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: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518484903 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001518484903 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518484903/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518484903/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518484903 Building ZINC001518638787 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518638787' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518638787 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001518638787 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518638787/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518638787 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/530 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(c2ccc(Br)cc2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001518638787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001518638787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518638787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001518638787 none CC1(c2ccc(Br)cc2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', '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, 1, 1, 1, 1, 17, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 27, 27, 21, 27, 27, 27, 16, 16, 9, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 16, 16, 16, 16, 16, 27, 27, 27, 27, 16, 16, 16, 16, 10, 10, 16, 16, 16, 16] 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]) total number of confs: 77 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518638787 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518638787/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518638787 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 531) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/531 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/531' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(c2ccc(Br)cc2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001518638787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001518638787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518638787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001518638787 none CC1(c2ccc(Br)cc2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', '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, 1, 1, 1, 1, 17, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 28, 28, 18, 28, 28, 28, 15, 15, 9, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 15, 15, 15, 15, 15, 28, 28, 28, 28, 15, 15, 15, 15, 10, 10, 15, 15, 15, 15] 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]) total number of confs: 90 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518638787 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001518638787 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518638787/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518638787/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518638787 Building ZINC001518638787 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518638787' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518638787 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001518638787 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518638787/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518638787 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 530) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC1(c2ccc(Br)cc2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001518638787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001518638787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518638787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001518638787 none CC1(c2ccc(Br)cc2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', '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, 1, 1, 1, 1, 17, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 27, 27, 21, 27, 27, 27, 16, 16, 9, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 16, 16, 16, 16, 16, 27, 27, 27, 27, 16, 16, 16, 16, 10, 10, 16, 16, 16, 16] 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]) total number of confs: 77 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518638787 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518638787/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518638787 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 531) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC1(c2ccc(Br)cc2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001518638787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001518638787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518638787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001518638787 none CC1(c2ccc(Br)cc2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', '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, 1, 1, 1, 1, 17, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 28, 28, 18, 28, 28, 28, 15, 15, 9, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 15, 15, 15, 15, 15, 28, 28, 28, 28, 15, 15, 15, 15, 10, 10, 15, 15, 15, 15] 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]) total number of confs: 90 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518638787 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001518638787 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518638787/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518638787/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518638787 Building ZINC001518838817 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518838817' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518838817 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001518838817 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518838817/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518838817 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/532 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(CN(C)C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1OCc1ccccc1F) `ZINC001518838817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001518838817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518838817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001518838817 none COc1cccc(CN(C)C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1OCc1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 12, 5, 1, 1, 1, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 7, 19, 30, 30, 21, 30, 30, 30, 8, 8, 8, 5, 5, 5, 5, 5, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 19, 19, 30, 30, 30, 30] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518838817 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518838817/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518838817 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 533) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/533 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/533' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(CN(C)C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1OCc1ccccc1F) `ZINC001518838817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001518838817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518838817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001518838817 none COc1cccc(CN(C)C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1OCc1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 12, 5, 1, 1, 1, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 7, 19, 30, 30, 24, 30, 30, 30, 8, 8, 8, 5, 5, 5, 5, 5, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 19, 19, 30, 30, 30, 30] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 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/12845/xbi-8058088.35/working/building/ZINC001518838817 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001518838817 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518838817/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518838817/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518838817 Building ZINC001518838817 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518838817' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518838817 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001518838817 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518838817/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518838817 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 532) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1cccc(CN(C)C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1OCc1ccccc1F) `ZINC001518838817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001518838817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518838817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001518838817 none COc1cccc(CN(C)C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1OCc1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 12, 5, 1, 1, 1, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 7, 19, 30, 30, 21, 30, 30, 30, 8, 8, 8, 5, 5, 5, 5, 5, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 19, 19, 30, 30, 30, 30] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518838817 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518838817/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518838817 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 533) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1cccc(CN(C)C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1OCc1ccccc1F) `ZINC001518838817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001518838817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518838817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001518838817 none COc1cccc(CN(C)C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1OCc1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 12, 5, 1, 1, 1, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 7, 19, 30, 30, 24, 30, 30, 30, 8, 8, 8, 5, 5, 5, 5, 5, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 19, 19, 30, 30, 30, 30] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 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/12845/xbi-8058088.35/working/building/ZINC001518838817 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001518838817 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518838817/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518838817/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518838817 Building ZINC001518970028 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970028' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970028 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001518970028 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970028/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970028 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/534 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@H]2c2cccc(Cl)c2)c1) `ZINC001518970028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001518970028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001518970028 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@H]2c2cccc(Cl)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.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 6, 6, 11, 11, 13, 13, 13, 13, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 14, 14, 14, 14, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970028 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970028/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970028 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 535) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/535 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/535' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@H]2c2cccc(Cl)c2)c1) `ZINC001518970028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001518970028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001518970028 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@H]2c2cccc(Cl)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.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 5, 5, 5, 8, 8, 12, 12, 12, 12, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 13, 13, 13, 13, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970028 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001518970028 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970028/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970028/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970028 Building ZINC001518970028 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970028' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970028 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001518970028 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970028/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970028 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 534) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@H]2c2cccc(Cl)c2)c1) `ZINC001518970028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001518970028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001518970028 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@H]2c2cccc(Cl)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.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 6, 6, 11, 11, 13, 13, 13, 13, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 14, 14, 14, 14, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970028 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970028/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970028 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 535) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@H]2c2cccc(Cl)c2)c1) `ZINC001518970028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001518970028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001518970028 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@H]2c2cccc(Cl)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.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 5, 5, 5, 8, 8, 12, 12, 12, 12, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5, 13, 13, 13, 13, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970028 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001518970028 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970028/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970028/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970028 Building ZINC001518970030 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970030' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970030 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001518970030 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970030/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970030 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/536 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@@H]2c2cccc(Cl)c2)c1) `ZINC001518970030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001518970030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001518970030 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@@H]2c2cccc(Cl)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.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 8, 8, 14, 14, 14, 14, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 2, 2, 2, 2, 1, 2, 2, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 12, 12, 12, 12, 2] 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, 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: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970030 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970030/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970030 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 537) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/537 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/537' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@@H]2c2cccc(Cl)c2)c1) `ZINC001518970030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001518970030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001518970030 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@@H]2c2cccc(Cl)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.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 6, 6, 6, 6, 6, 11, 11, 12, 12, 12, 12, 6, 6, 6, 6, 17, 17, 13, 17, 17, 17, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 17, 17, 17, 17, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970030 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001518970030 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970030/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970030/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970030 Building ZINC001518970030 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970030' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970030 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001518970030 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970030/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970030 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 536) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@@H]2c2cccc(Cl)c2)c1) `ZINC001518970030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001518970030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001518970030 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@@H]2c2cccc(Cl)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.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 8, 8, 14, 14, 14, 14, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 2, 2, 2, 2, 1, 2, 2, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 12, 12, 12, 12, 2] 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, 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: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970030 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970030/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970030 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 537) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@@H]2c2cccc(Cl)c2)c1) `ZINC001518970030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001518970030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001518970030 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)OC(C)(C)C)C[C@@H]2c2cccc(Cl)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.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 6, 6, 6, 6, 6, 11, 11, 12, 12, 12, 12, 6, 6, 6, 6, 17, 17, 13, 17, 17, 17, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 17, 17, 17, 17, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970030 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001518970030 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970030/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970030/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001518970030 Building ZINC001519180074 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519180074' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519180074 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001519180074 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519180074/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519180074 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/538 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)ccc1Oc1ccc(F)cc1) `ZINC001519180074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001519180074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519180074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001519180074 none Cc1cc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)ccc1Oc1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 21, 21, 47, 47, 47, 47, 47, 47, 47, 31, 31, 31, 31, 11, 11, 2, 4, 4, 4, 4, 4, 4, 4, 31, 31, 47, 47, 47, 47] 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519180074 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519180074/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519180074 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 539) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/539 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/539' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CNC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)ccc1Oc1ccc(F)cc1) `ZINC001519180074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001519180074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519180074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001519180074 none Cc1cc(CNC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)ccc1Oc1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 21, 21, 47, 47, 47, 47, 47, 47, 47, 31, 31, 31, 31, 11, 11, 2, 4, 4, 4, 4, 4, 4, 4, 31, 31, 47, 47, 47, 47] 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519180074 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001519180074 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519180074/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519180074/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519180074 Building ZINC001519180074 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519180074' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519180074 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001519180074 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519180074/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519180074 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 538) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1cc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)ccc1Oc1ccc(F)cc1) `ZINC001519180074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001519180074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519180074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001519180074 none Cc1cc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)ccc1Oc1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 21, 21, 47, 47, 47, 47, 47, 47, 47, 31, 31, 31, 31, 11, 11, 2, 4, 4, 4, 4, 4, 4, 4, 31, 31, 47, 47, 47, 47] 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519180074 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519180074/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519180074 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 539) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1cc(CNC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)ccc1Oc1ccc(F)cc1) `ZINC001519180074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001519180074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519180074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001519180074 none Cc1cc(CNC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)ccc1Oc1ccc(F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 21, 21, 47, 47, 47, 47, 47, 47, 47, 31, 31, 31, 31, 11, 11, 2, 4, 4, 4, 4, 4, 4, 4, 31, 31, 47, 47, 47, 47] 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519180074 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001519180074 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519180074/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519180074/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519180074 Building ZINC001519348171 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348171' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348171 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001519348171 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348171/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348171 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/540 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(C(F)(F)F)c2ccccc2CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001519348171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001519348171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001519348171 none C[C@@]1(C(F)(F)F)c2ccccc2CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'F', 'F', '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.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: [5, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 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] 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] 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: [14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 1, 11, 1, 1, 1, 10, 10, 10, 10, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 10, 10] 29 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]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348171 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348171/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348171 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 541) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/541 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/541' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(C(F)(F)F)c2ccccc2CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001519348171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001519348171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001519348171 none C[C@@]1(C(F)(F)F)c2ccccc2CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'F', 'F', '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.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: [5, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 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] 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] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 1, 9, 1, 1, 1, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9] 23 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]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348171 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001519348171 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348171/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348171/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348171 Building ZINC001519348171 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348171' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348171 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001519348171 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348171/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348171 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 540) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@@]1(C(F)(F)F)c2ccccc2CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001519348171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001519348171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001519348171 none C[C@@]1(C(F)(F)F)c2ccccc2CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'F', 'F', '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.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: [5, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 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] 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] 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: [14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 1, 11, 1, 1, 1, 10, 10, 10, 10, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 10, 10] 29 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]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348171 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348171/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348171 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 541) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@@]1(C(F)(F)F)c2ccccc2CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001519348171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001519348171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001519348171 none C[C@@]1(C(F)(F)F)c2ccccc2CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'F', 'F', '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.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: [5, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 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] 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] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 1, 9, 1, 1, 1, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9] 23 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]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348171 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001519348171 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348171/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348171/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348171 Building ZINC001519348176 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348176' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348176 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001519348176 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348176/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348176 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/542 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(C(F)(F)F)c2ccccc2CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001519348176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001519348176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001519348176 none C[C@]1(C(F)(F)F)c2ccccc2CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'F', 'F', '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.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: [5, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 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] 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] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 1, 9, 1, 1, 1, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9] 23 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]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348176 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348176/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348176 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 543) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/543 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/543' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(C(F)(F)F)c2ccccc2CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001519348176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001519348176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001519348176 none C[C@]1(C(F)(F)F)c2ccccc2CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'F', 'F', '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.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: [5, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 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] 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] 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: [14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 1, 11, 1, 1, 1, 10, 10, 10, 10, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 10, 10] 28 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]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348176 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001519348176 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348176/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348176/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348176 Building ZINC001519348176 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348176' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348176 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001519348176 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348176/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348176 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 542) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@]1(C(F)(F)F)c2ccccc2CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001519348176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001519348176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001519348176 none C[C@]1(C(F)(F)F)c2ccccc2CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'F', 'F', '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.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: [5, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 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] 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] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 1, 9, 1, 1, 1, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9] 23 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]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348176 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348176/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348176 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 543) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@]1(C(F)(F)F)c2ccccc2CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001519348176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001519348176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001519348176 none C[C@]1(C(F)(F)F)c2ccccc2CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'F', 'F', '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.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: [5, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 1, 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] 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] 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: [14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 1, 11, 1, 1, 1, 10, 10, 10, 10, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 10, 10] 28 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]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348176 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001519348176 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348176/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348176/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519348176 Building ZINC001519369793 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519369793' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519369793 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001519369793 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519369793/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519369793 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/544 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(c2cccc(Cl)c2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001519369793.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001519369793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519369793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001519369793 none CC1(c2cccc(Cl)c2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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', '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, 1, 1, 1, 1, 1, 16, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 32, 32, 32, 10, 10, 6, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 32, 32, 32, 32, 10, 10, 10, 10, 3, 3, 10, 10, 10, 10] 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519369793 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519369793/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519369793 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 545) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/545 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/545' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(c2cccc(Cl)c2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001519369793.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001519369793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519369793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001519369793 none CC1(c2cccc(Cl)c2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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', '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, 1, 1, 1, 1, 1, 16, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 30, 30, 30, 30, 30, 10, 10, 6, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 30, 30, 30, 30, 10, 10, 10, 10, 3, 3, 10, 10, 10, 10] 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]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519369793 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001519369793 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519369793/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519369793/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519369793 Building ZINC001519369793 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519369793' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519369793 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001519369793 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519369793/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519369793 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 544) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC1(c2cccc(Cl)c2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001519369793.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001519369793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519369793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001519369793 none CC1(c2cccc(Cl)c2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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', '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, 1, 1, 1, 1, 1, 16, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 32, 32, 32, 10, 10, 6, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 32, 32, 32, 32, 10, 10, 10, 10, 3, 3, 10, 10, 10, 10] 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519369793 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519369793/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519369793 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 545) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC1(c2cccc(Cl)c2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001519369793.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001519369793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519369793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001519369793 none CC1(c2cccc(Cl)c2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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', '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, 1, 1, 1, 1, 1, 16, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 30, 30, 30, 30, 30, 10, 10, 6, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 30, 30, 30, 30, 10, 10, 10, 10, 3, 3, 10, 10, 10, 10] 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]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519369793 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001519369793 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519369793/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519369793/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519369793 Building ZINC001519411798 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519411798' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519411798 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001519411798 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519411798/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519411798 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/546 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/546' -> `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)NCc1ccccc1Oc1ccccc1) `ZINC001519411798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001519411798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519411798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001519411798 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1Oc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 5, 1, 1, 1, 1, 1, 1, 12, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 13, 31, 31, 28, 31, 31, 31, 44, 46, 46, 45, 46, 46, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 13, 13, 31, 31, 31, 31, 46, 46, 45, 46, 46] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 134 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519411798 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519411798/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519411798 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 547) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/547 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/547' -> `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)NCc1ccccc1Oc1ccccc1) `ZINC001519411798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001519411798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519411798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001519411798 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1Oc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 5, 1, 1, 1, 1, 1, 1, 12, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 13, 29, 29, 20, 29, 29, 29, 43, 47, 47, 43, 47, 47, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 13, 13, 29, 29, 29, 29, 47, 47, 45, 47, 47] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519411798 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001519411798 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519411798/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519411798/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519411798 Building ZINC001519411798 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519411798' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519411798 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001519411798 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519411798/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519411798 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 546) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/546: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1Oc1ccccc1) `ZINC001519411798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001519411798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519411798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001519411798 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1Oc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 5, 1, 1, 1, 1, 1, 1, 12, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 13, 31, 31, 28, 31, 31, 31, 44, 46, 46, 45, 46, 46, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 13, 13, 31, 31, 31, 31, 46, 46, 45, 46, 46] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 134 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519411798 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519411798/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519411798 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 547) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/547: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1Oc1ccccc1) `ZINC001519411798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001519411798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519411798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001519411798 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1Oc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 5, 1, 1, 1, 1, 1, 1, 12, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 13, 29, 29, 20, 29, 29, 29, 43, 47, 47, 43, 47, 47, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 13, 13, 29, 29, 29, 29, 47, 47, 45, 47, 47] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519411798 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001519411798 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519411798/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519411798/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519411798 Building ZINC001519558886 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519558886' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519558886 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001519558886 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519558886/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519558886 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/548 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1csc(Br)c1)C1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001519558886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001519558886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519558886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001519558886 none O=C(N(Cc1csc(Br)c1)C1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'Br', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 14, 1, 17, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [4, 1, 4, 8, 16, 34, 34, 34, 34, 34, 8, 11, 11, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 34, 34, 11, 11, 11, 11, 11, 5, 5] 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]) total number of confs: 110 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519558886 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519558886/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519558886 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 549) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/549 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/549' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1csc(Br)c1)C1CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001519558886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001519558886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519558886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001519558886 none O=C(N(Cc1csc(Br)c1)C1CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'Br', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 14, 1, 17, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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, 6, 15, 34, 34, 34, 34, 34, 6, 10, 10, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 34, 34, 10, 10, 10, 10, 10, 4, 4] 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]) total number of confs: 114 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519558886 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001519558886 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519558886/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519558886/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519558886 Building ZINC001519558886 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519558886' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519558886 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001519558886 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519558886/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519558886 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 548) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N(Cc1csc(Br)c1)C1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001519558886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001519558886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519558886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001519558886 none O=C(N(Cc1csc(Br)c1)C1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'Br', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 14, 1, 17, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [4, 1, 4, 8, 16, 34, 34, 34, 34, 34, 8, 11, 11, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 34, 34, 11, 11, 11, 11, 11, 5, 5] 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]) total number of confs: 110 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519558886 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519558886/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519558886 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 549) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N(Cc1csc(Br)c1)C1CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001519558886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001519558886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519558886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001519558886 none O=C(N(Cc1csc(Br)c1)C1CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'Br', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 14, 1, 17, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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, 6, 15, 34, 34, 34, 34, 34, 6, 10, 10, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 34, 34, 10, 10, 10, 10, 10, 4, 4] 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]) total number of confs: 114 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519558886 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001519558886 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519558886/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519558886/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519558886 Building ZINC001519561550 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519561550' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519561550 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001519561550 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519561550/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519561550 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/550 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(F)(c2ccccc2OC(F)(F)F)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001519561550.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001519561550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519561550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001519561550 none O=C(N1CCC(F)(c2ccccc2OC(F)(F)F)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 7, 7, 7, 7, 17, 17, 9, 17, 17, 17, 30, 30, 30, 30, 7, 7, 1, 1, 1, 3, 3, 5, 5, 3, 5, 5, 5, 7, 7, 7, 7, 17, 17, 17, 17, 7, 7, 7, 7, 3, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519561550 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519561550/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519561550 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 551) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/551 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/551' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(F)(c2ccccc2OC(F)(F)F)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001519561550.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001519561550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519561550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001519561550 none O=C(N1CCC(F)(c2ccccc2OC(F)(F)F)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 26, 26, 26, 26, 3, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 13, 13, 13, 13, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 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, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519561550 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001519561550 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519561550/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519561550/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519561550 Building ZINC001519561550 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519561550' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519561550 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001519561550 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519561550/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519561550 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 550) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(N1CCC(F)(c2ccccc2OC(F)(F)F)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001519561550.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001519561550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519561550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001519561550 none O=C(N1CCC(F)(c2ccccc2OC(F)(F)F)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 7, 7, 7, 7, 17, 17, 9, 17, 17, 17, 30, 30, 30, 30, 7, 7, 1, 1, 1, 3, 3, 5, 5, 3, 5, 5, 5, 7, 7, 7, 7, 17, 17, 17, 17, 7, 7, 7, 7, 3, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519561550 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519561550/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519561550 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 551) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(N1CCC(F)(c2ccccc2OC(F)(F)F)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001519561550.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001519561550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519561550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001519561550 none O=C(N1CCC(F)(c2ccccc2OC(F)(F)F)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 26, 26, 26, 26, 3, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 13, 13, 13, 13, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 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, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519561550 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001519561550 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519561550/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519561550/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519561550 Building ZINC001519633784 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633784' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633784 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001519633784 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633784/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633784 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/552 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cc(Br)ccc2O1) `ZINC001519633784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001519633784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001519633784 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cc(Br)ccc2O1 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', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 1, 1, 1, 17, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 20, 3, 20, 1, 1, 1, 5, 5, 5, 2, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 2, 5, 30, 30, 30] 37 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633784 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633784/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633784 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 553) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/553 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/553' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cc(Br)ccc2O1) `ZINC001519633784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001519633784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001519633784 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cc(Br)ccc2O1 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', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 1, 1, 1, 17, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 21, 3, 21, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 5, 1, 5, 31, 31, 31] 37 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633784 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001519633784 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633784/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633784/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633784 Building ZINC001519633784 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633784' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633784 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001519633784 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633784/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633784 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 552) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/552: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cc(Br)ccc2O1) `ZINC001519633784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001519633784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001519633784 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cc(Br)ccc2O1 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', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 1, 1, 1, 17, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 20, 3, 20, 1, 1, 1, 5, 5, 5, 2, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 2, 5, 30, 30, 30] 37 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633784 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633784/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633784 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 553) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/553: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cc(Br)ccc2O1) `ZINC001519633784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001519633784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001519633784 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cc(Br)ccc2O1 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', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 1, 1, 1, 17, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 21, 3, 21, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 5, 1, 5, 31, 31, 31] 37 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633784 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001519633784 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633784/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633784/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633784 Building ZINC001519633785 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633785' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633785 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001519633785 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633785/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633785 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/554 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cc(Br)ccc2O1) `ZINC001519633785.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001519633785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001519633785 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cc(Br)ccc2O1 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', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 1, 1, 1, 17, 1, 1, 1, 12, 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, 3, 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: [30, 30, 30, 30, 20, 3, 20, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 2, 5, 30, 30, 30] 35 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633785 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633785/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633785 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 555) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/555 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/555' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cc(Br)ccc2O1) `ZINC001519633785.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001519633785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633785/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001519633785 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cc(Br)ccc2O1 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', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 1, 1, 1, 17, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 20, 3, 20, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 1, 5, 29, 29, 29] 36 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633785 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001519633785 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633785/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633785/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633785 Building ZINC001519633785 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633785' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633785 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001519633785 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633785/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633785 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 554) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/554: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2cc(Cl)cc(Cl)c2)c2cc(Br)ccc2O1) `ZINC001519633785.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001519633785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001519633785 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cc(Br)ccc2O1 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', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 1, 1, 1, 17, 1, 1, 1, 12, 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, 3, 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: [30, 30, 30, 30, 20, 3, 20, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 2, 5, 30, 30, 30] 35 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633785 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633785/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633785 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 555) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2cc(Cl)cc(Cl)c2)c2cc(Br)ccc2O1) `ZINC001519633785.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001519633785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633785/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001519633785 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cc(Br)ccc2O1 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', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 1, 1, 1, 17, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 20, 3, 20, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 1, 5, 29, 29, 29] 36 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633785 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001519633785 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633785/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633785/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519633785 Building ZINC001519684070 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519684070' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519684070 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001519684070 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519684070/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519684070 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/556 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/556' -> `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)c1ccc(C)c(C)c1) `ZINC001519684070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001519684070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519684070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001519684070 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)c1ccc(C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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.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, 1, 5, 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, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 4, 4, 10, 10, 4, 4, 10, 10, 10, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 4, 4, 4, 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: 95 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519684070 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519684070/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519684070 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 557) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/557 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/557' -> `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)c1ccc(C)c(C)c1) `ZINC001519684070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001519684070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519684070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001519684070 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)c1ccc(C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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.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, 1, 5, 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, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 4, 4, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 4, 4, 4, 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: 51 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519684070 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001519684070 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519684070/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519684070/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519684070 Building ZINC001519684070 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519684070' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519684070 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001519684070 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519684070/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519684070 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 556) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)c1ccc(C)c(C)c1) `ZINC001519684070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001519684070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519684070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001519684070 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)c1ccc(C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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.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, 1, 5, 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, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 4, 4, 10, 10, 4, 4, 10, 10, 10, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 4, 4, 4, 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: 95 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519684070 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519684070/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519684070 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 557) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/557: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)c1ccc(C)c(C)c1) `ZINC001519684070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001519684070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519684070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001519684070 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)c1ccc(C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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.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, 1, 5, 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, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 4, 4, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 4, 4, 4, 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: 51 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519684070 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001519684070 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519684070/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519684070/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519684070 Building ZINC001519693458 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519693458' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519693458 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001519693458 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519693458/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519693458 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/558 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Oc2ccc(CCNC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)cc2)cc1) `ZINC001519693458.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001519693458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519693458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001519693458 none COc1ccc(Oc2ccc(CCNC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 17, 12, 7, 12, 12, 7, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 3, 4, 8, 4, 4, 4, 12, 12, 26, 26, 26, 26, 26, 26, 26, 12, 12, 7, 7, 4, 4, 2, 4, 4, 8, 8, 8, 4, 12, 12, 26, 26] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519693458 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519693458/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519693458 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 559) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/559 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/559' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Oc2ccc(CCNC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)cc2)cc1) `ZINC001519693458.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001519693458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519693458/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001519693458 none COc1ccc(Oc2ccc(CCNC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 18, 18, 27, 27, 18, 8, 8, 13, 13, 8, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 3, 4, 8, 4, 4, 4, 13, 13, 27, 27, 27, 27, 27, 27, 27, 13, 13, 8, 8, 5, 5, 2, 4, 4, 8, 8, 8, 4, 13, 13, 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, 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/12845/xbi-8058088.35/working/building/ZINC001519693458 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001519693458 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519693458/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519693458/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519693458 Building ZINC001519693458 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519693458' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519693458 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001519693458 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519693458/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519693458 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 558) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc(Oc2ccc(CCNC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)cc2)cc1) `ZINC001519693458.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001519693458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519693458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001519693458 none COc1ccc(Oc2ccc(CCNC(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 17, 12, 7, 12, 12, 7, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 3, 4, 8, 4, 4, 4, 12, 12, 26, 26, 26, 26, 26, 26, 26, 12, 12, 7, 7, 4, 4, 2, 4, 4, 8, 8, 8, 4, 12, 12, 26, 26] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519693458 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519693458/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519693458 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 559) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc(Oc2ccc(CCNC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)cc2)cc1) `ZINC001519693458.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001519693458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519693458/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001519693458 none COc1ccc(Oc2ccc(CCNC(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 18, 18, 27, 27, 18, 8, 8, 13, 13, 8, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 3, 4, 8, 4, 4, 4, 13, 13, 27, 27, 27, 27, 27, 27, 27, 13, 13, 8, 8, 5, 5, 2, 4, 4, 8, 8, 8, 4, 13, 13, 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, 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/12845/xbi-8058088.35/working/building/ZINC001519693458 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001519693458 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519693458/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519693458/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519693458 Building ZINC001519809300 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519809300' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519809300 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001519809300 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519809300/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519809300 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/560 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cc2cc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2s1) `ZINC001519809300.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001519809300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519809300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001519809300 none CCOC(=O)c1cc2cc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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, 5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 14, 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, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 9, 21, 9, 9, 9, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 9, 9, 9, 9, 33, 33, 33, 33, 33, 9, 9, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 9, 9] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519809300 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519809300/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519809300 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 561) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/561 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/561' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cc2cc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2s1) `ZINC001519809300.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001519809300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519809300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001519809300 none CCOC(=O)c1cc2cc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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, 5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 14, 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, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 20, 20, 9, 20, 9, 9, 9, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 9, 9, 9, 9, 31, 31, 31, 31, 31, 9, 9, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 9, 9] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519809300 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001519809300 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519809300/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519809300/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519809300 Building ZINC001519809300 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519809300' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519809300 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001519809300 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519809300/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519809300 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 560) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOC(=O)c1cc2cc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2s1) `ZINC001519809300.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001519809300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519809300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001519809300 none CCOC(=O)c1cc2cc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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, 5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 14, 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, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 9, 21, 9, 9, 9, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 9, 9, 9, 9, 33, 33, 33, 33, 33, 9, 9, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 9, 9] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519809300 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519809300/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519809300 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 561) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOC(=O)c1cc2cc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2s1) `ZINC001519809300.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001519809300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519809300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001519809300 none CCOC(=O)c1cc2cc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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, 5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 14, 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, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 20, 20, 9, 20, 9, 9, 9, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 9, 9, 9, 9, 31, 31, 31, 31, 31, 9, 9, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 9, 9] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519809300 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001519809300 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519809300/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519809300/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519809300 Building ZINC001519823975 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519823975' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519823975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001519823975 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519823975/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519823975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/562 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Oc2ncc(Cl)cn2)c(Cl)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001519823975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001519823975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519823975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001519823975 none O=C(Nc1ccc(Oc2ncc(Cl)cn2)c(Cl)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 8, 1, 1, 16, 1, 8, 1, 16, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 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, 10, 10, 10, 10, 26, 26, 26, 26, 26, 26, 26, 10, 10, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 26, 26, 10, 4, 4, 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519823975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519823975/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519823975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 563) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/563 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/563' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Oc2ncc(Cl)cn2)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001519823975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001519823975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519823975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001519823975 none O=C(Nc1ccc(Oc2ncc(Cl)cn2)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 8, 1, 1, 16, 1, 8, 1, 16, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 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, 10, 10, 8, 10, 26, 26, 26, 26, 26, 26, 26, 10, 10, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 26, 26, 10, 4, 4, 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519823975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001519823975 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519823975/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519823975/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519823975 Building ZINC001519823975 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519823975' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519823975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001519823975 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519823975/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519823975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 562) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/562: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Oc2ncc(Cl)cn2)c(Cl)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001519823975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001519823975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519823975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001519823975 none O=C(Nc1ccc(Oc2ncc(Cl)cn2)c(Cl)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 8, 1, 1, 16, 1, 8, 1, 16, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 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, 10, 10, 10, 10, 26, 26, 26, 26, 26, 26, 26, 10, 10, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 26, 26, 10, 4, 4, 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]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519823975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519823975/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519823975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 563) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/563: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Oc2ncc(Cl)cn2)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001519823975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001519823975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519823975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001519823975 none O=C(Nc1ccc(Oc2ncc(Cl)cn2)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 8, 1, 1, 16, 1, 8, 1, 16, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 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, 10, 10, 8, 10, 26, 26, 26, 26, 26, 26, 26, 10, 10, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 26, 26, 10, 4, 4, 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519823975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001519823975 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519823975/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519823975/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519823975 Building ZINC001519831246 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519831246' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519831246 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001519831246 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519831246/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519831246 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/564 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/564' -> `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])c1ccc2c(c1)CCC2) `ZINC001519831246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001519831246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519831246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001519831246 none O=C(NCC1(c2cccc(Br)c2)CCCC1)[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', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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] 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 26, 26, 26, 26, 26, 26, 15, 15, 15, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 26, 26, 26, 26, 15, 15, 15, 15, 15, 15, 15, 15, 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, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519831246 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519831246/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519831246 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 565) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/565 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/565' -> `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])c1ccc2c(c1)CCC2) `ZINC001519831246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001519831246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519831246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001519831246 none O=C(NCC1(c2cccc(Br)c2)CCCC1)[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', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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] 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 18, 28, 28, 28, 28, 28, 28, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 8, 8, 28, 28, 28, 28, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6, 6, 6, 6, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519831246 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001519831246 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519831246/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519831246/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519831246 Building ZINC001519831246 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519831246' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519831246 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001519831246 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519831246/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519831246 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 564) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NCC1(c2cccc(Br)c2)CCCC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001519831246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001519831246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519831246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001519831246 none O=C(NCC1(c2cccc(Br)c2)CCCC1)[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', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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] 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 26, 26, 26, 26, 26, 26, 15, 15, 15, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 26, 26, 26, 26, 15, 15, 15, 15, 15, 15, 15, 15, 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, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519831246 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519831246/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519831246 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 565) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NCC1(c2cccc(Br)c2)CCCC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001519831246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001519831246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519831246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001519831246 none O=C(NCC1(c2cccc(Br)c2)CCCC1)[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', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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] 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 18, 28, 28, 28, 28, 28, 28, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 8, 8, 28, 28, 28, 28, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6, 6, 6, 6, 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, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519831246 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001519831246 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519831246/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519831246/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519831246 Building ZINC001519851904 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519851904' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519851904 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001519851904 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519851904/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519851904 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/566 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(Cc2ccccc2Br)cs1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001519851904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001519851904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519851904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001519851904 none O=C(Nc1nc(Cc2ccccc2Br)cs1)[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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', '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, 5, 1, 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, 20, 26, 26, 26, 26, 26, 26, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 2, 20, 20, 26, 26, 26, 26, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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/12845/xbi-8058088.35/working/building/ZINC001519851904 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519851904/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519851904 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 567) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/567 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/567' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(Cc2ccccc2Br)cs1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001519851904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001519851904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519851904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001519851904 none O=C(Nc1nc(Cc2ccccc2Br)cs1)[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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', '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, 5, 1, 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, 20, 25, 25, 25, 25, 25, 25, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 2, 20, 20, 25, 25, 25, 25, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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/12845/xbi-8058088.35/working/building/ZINC001519851904 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001519851904 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519851904/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519851904/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519851904 Building ZINC001519851904 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519851904' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519851904 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001519851904 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519851904/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519851904 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 566) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/566: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(Cc2ccccc2Br)cs1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001519851904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001519851904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519851904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001519851904 none O=C(Nc1nc(Cc2ccccc2Br)cs1)[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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', '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, 5, 1, 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, 20, 26, 26, 26, 26, 26, 26, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 2, 20, 20, 26, 26, 26, 26, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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/12845/xbi-8058088.35/working/building/ZINC001519851904 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519851904/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519851904 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 567) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/567: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(Cc2ccccc2Br)cs1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001519851904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001519851904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519851904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001519851904 none O=C(Nc1nc(Cc2ccccc2Br)cs1)[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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', '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, 5, 1, 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, 20, 25, 25, 25, 25, 25, 25, 4, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 2, 20, 20, 25, 25, 25, 25, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5] 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/12845/xbi-8058088.35/working/building/ZINC001519851904 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001519851904 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519851904/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519851904/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519851904 Building ZINC001519864192 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519864192' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519864192 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001519864192 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519864192/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519864192 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/568 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)ccc2OC(C)C)cc1Cl) `ZINC001519864192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001519864192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519864192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001519864192 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)ccc2OC(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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 17, 1, 1, 1, 12, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [11, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 3, 7, 7, 7, 21, 28, 28, 4, 4, 4, 11, 11, 11, 4, 4, 3, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 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/12845/xbi-8058088.35/working/building/ZINC001519864192 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519864192/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519864192 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 569) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/569 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/569' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)ccc2OC(C)C)cc1Cl) `ZINC001519864192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001519864192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519864192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001519864192 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)ccc2OC(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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 17, 1, 1, 1, 12, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [11, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 3, 7, 7, 7, 21, 28, 28, 4, 4, 4, 11, 11, 11, 4, 4, 3, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 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/12845/xbi-8058088.35/working/building/ZINC001519864192 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001519864192 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519864192/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519864192/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519864192 Building ZINC001519864192 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519864192' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519864192 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001519864192 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519864192/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519864192 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 568) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)ccc2OC(C)C)cc1Cl) `ZINC001519864192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001519864192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519864192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001519864192 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)ccc2OC(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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 17, 1, 1, 1, 12, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [11, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 3, 7, 7, 7, 21, 28, 28, 4, 4, 4, 11, 11, 11, 4, 4, 3, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 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/12845/xbi-8058088.35/working/building/ZINC001519864192 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519864192/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519864192 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 569) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)ccc2OC(C)C)cc1Cl) `ZINC001519864192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001519864192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519864192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001519864192 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)ccc2OC(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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 17, 1, 1, 1, 12, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [11, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 3, 7, 7, 7, 21, 28, 28, 4, 4, 4, 11, 11, 11, 4, 4, 3, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 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/12845/xbi-8058088.35/working/building/ZINC001519864192 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001519864192 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519864192/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519864192/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001519864192 Building ZINC001520004865 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520004865' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520004865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520004865 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520004865/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520004865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/570 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc(C)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)s1) `ZINC001520004865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520004865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520004865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520004865 none CCc1nc(C)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.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 8, 1, 5, 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, 7, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 7, 12, 12, 12, 12, 12, 7, 7, 7, 2, 3, 3, 3, 16, 16, 3, 16, 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520004865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520004865/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520004865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 571) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/571 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/571' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc(C)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)s1) `ZINC001520004865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520004865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520004865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520004865 none CCc1nc(C)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.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 8, 1, 5, 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, 7, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 13, 13, 2, 13, 13, 13, 13, 13, 13, 2, 2, 7, 13, 13, 13, 13, 13, 7, 7, 7, 2, 2, 2, 2, 13, 13, 2, 13, 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: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520004865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520004865 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520004865/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520004865/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520004865 Building ZINC001520004865 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520004865' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520004865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520004865 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520004865/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520004865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 570) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/570: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc(C)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)s1) `ZINC001520004865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520004865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520004865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520004865 none CCc1nc(C)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.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 8, 1, 5, 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, 7, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 7, 12, 12, 12, 12, 12, 7, 7, 7, 2, 3, 3, 3, 16, 16, 3, 16, 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520004865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520004865/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520004865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 571) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/571: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc(C)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)s1) `ZINC001520004865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520004865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520004865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520004865 none CCc1nc(C)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.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 8, 1, 5, 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, 7, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 13, 13, 2, 13, 13, 13, 13, 13, 13, 2, 2, 7, 13, 13, 13, 13, 13, 7, 7, 7, 2, 2, 2, 2, 13, 13, 2, 13, 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: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520004865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520004865 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520004865/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520004865/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520004865 Building ZINC001520018630 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001520018630 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/572 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@H]1CCCCO1) `ZINC001520018630.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520018630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001520018630 none CC(C)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 11, 10, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 34, 43, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 34, 27, 27, 15, 15, 3, 3, 3, 3, 3, 15, 15, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 573) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/573 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/573' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@H]1CCCCO1) `ZINC001520018630.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520018630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001520018630 none CC(C)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 11, 10, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 34, 43, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 34, 27, 27, 15, 15, 3, 3, 3, 3, 3, 15, 15, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 574) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/574 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/574' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@H]1CCCCO1) `ZINC001520018630.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001520018630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001520018630 none CC(C)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 21, 3, 3, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 32, 42, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32, 32, 32, 21, 21, 15, 15, 3, 3, 3, 3, 3, 15, 15, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 575) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/575 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/575' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@H]1CCCCO1) `ZINC001520018630.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001520018630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001520018630 none CC(C)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 21, 3, 3, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 32, 42, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32, 32, 32, 21, 21, 15, 15, 3, 3, 3, 3, 3, 15, 15, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520018630 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 Building ZINC001520018630 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001520018630 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 572) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@H]1CCCCO1) `ZINC001520018630.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520018630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001520018630 none CC(C)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 11, 10, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 34, 43, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 34, 27, 27, 15, 15, 3, 3, 3, 3, 3, 15, 15, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 573) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@H]1CCCCO1) `ZINC001520018630.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520018630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001520018630 none CC(C)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 11, 10, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 34, 43, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 34, 27, 27, 15, 15, 3, 3, 3, 3, 3, 15, 15, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 574) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/574: 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)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@H]1CCCCO1) `ZINC001520018630.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001520018630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001520018630 none CC(C)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 21, 3, 3, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 32, 42, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32, 32, 32, 21, 21, 15, 15, 3, 3, 3, 3, 3, 15, 15, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 575) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/575: 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)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@H]1CCCCO1) `ZINC001520018630.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001520018630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001520018630 none CC(C)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 21, 3, 3, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 32, 42, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32, 32, 32, 21, 21, 15, 15, 3, 3, 3, 3, 3, 15, 15, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520018630 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 Building ZINC001520018630 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001520018630 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 572) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@H]1CCCCO1) `ZINC001520018630.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520018630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001520018630 none CC(C)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 11, 10, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 34, 43, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 34, 27, 27, 15, 15, 3, 3, 3, 3, 3, 15, 15, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 573) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@H]1CCCCO1) `ZINC001520018630.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520018630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001520018630 none CC(C)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 11, 10, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 34, 43, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 34, 27, 27, 15, 15, 3, 3, 3, 3, 3, 15, 15, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 574) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/574: 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)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@H]1CCCCO1) `ZINC001520018630.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001520018630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001520018630 none CC(C)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 21, 3, 3, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 32, 42, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32, 32, 32, 21, 21, 15, 15, 3, 3, 3, 3, 3, 15, 15, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 575) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/575: 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)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@H]1CCCCO1) `ZINC001520018630.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001520018630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001520018630 none CC(C)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 21, 3, 3, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 32, 42, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32, 32, 32, 21, 21, 15, 15, 3, 3, 3, 3, 3, 15, 15, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520018630 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 Building ZINC001520018630 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001520018630 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 572) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@H]1CCCCO1) `ZINC001520018630.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520018630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001520018630 none CC(C)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 11, 10, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 34, 43, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 34, 27, 27, 15, 15, 3, 3, 3, 3, 3, 15, 15, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 573) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@H]1CCCCO1) `ZINC001520018630.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520018630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001520018630 none CC(C)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 11, 10, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 34, 43, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 34, 27, 27, 15, 15, 3, 3, 3, 3, 3, 15, 15, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 574) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/574: 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)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@H]1CCCCO1) `ZINC001520018630.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001520018630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001520018630 none CC(C)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 21, 3, 3, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 32, 42, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32, 32, 32, 21, 21, 15, 15, 3, 3, 3, 3, 3, 15, 15, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 575) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/575: 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)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@H]1CCCCO1) `ZINC001520018630.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001520018630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001520018630 none CC(C)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 21, 3, 3, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 32, 42, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 32, 32, 32, 21, 21, 15, 15, 3, 3, 3, 3, 3, 15, 15, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520018630 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018630 Building ZINC001520018632 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001520018632 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/576 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@@H]1CCCCO1) `ZINC001520018632.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520018632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001520018632 none CC(C)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 14, 9, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 33, 44, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 33, 33, 25, 25, 15, 15, 3, 3, 3, 3, 3, 15, 15, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 577) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/577 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/577' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@@H]1CCCCO1) `ZINC001520018632.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520018632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001520018632 none CC(C)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 14, 9, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 33, 44, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 33, 33, 25, 25, 15, 15, 3, 3, 3, 3, 3, 15, 15, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 578) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/578 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/578' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@@H]1CCCCO1) `ZINC001520018632.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001520018632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001520018632 none CC(C)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 10, 10, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 34, 43, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 34, 27, 27, 15, 15, 3, 3, 3, 3, 3, 15, 15, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 579) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/579 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/579' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@@H]1CCCCO1) `ZINC001520018632.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001520018632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001520018632 none CC(C)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 10, 10, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 34, 43, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 34, 27, 27, 15, 15, 3, 3, 3, 3, 3, 15, 15, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520018632 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 Building ZINC001520018632 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001520018632 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 576) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@@H]1CCCCO1) `ZINC001520018632.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520018632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001520018632 none CC(C)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 14, 9, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 33, 44, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 33, 33, 25, 25, 15, 15, 3, 3, 3, 3, 3, 15, 15, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 577) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@@H]1CCCCO1) `ZINC001520018632.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520018632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001520018632 none CC(C)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 14, 9, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 33, 44, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 33, 33, 25, 25, 15, 15, 3, 3, 3, 3, 3, 15, 15, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 578) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/578: 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)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@@H]1CCCCO1) `ZINC001520018632.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001520018632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001520018632 none CC(C)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 10, 10, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 34, 43, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 34, 27, 27, 15, 15, 3, 3, 3, 3, 3, 15, 15, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 579) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/579: 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)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@@H]1CCCCO1) `ZINC001520018632.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001520018632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001520018632 none CC(C)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 10, 10, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 34, 43, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 34, 27, 27, 15, 15, 3, 3, 3, 3, 3, 15, 15, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520018632 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 Building ZINC001520018632 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001520018632 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 576) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@@H]1CCCCO1) `ZINC001520018632.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520018632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001520018632 none CC(C)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 14, 9, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 33, 44, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 33, 33, 25, 25, 15, 15, 3, 3, 3, 3, 3, 15, 15, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 577) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@@H]1CCCCO1) `ZINC001520018632.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520018632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001520018632 none CC(C)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 14, 9, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 33, 44, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 33, 33, 25, 25, 15, 15, 3, 3, 3, 3, 3, 15, 15, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 578) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/578: 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)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@@H]1CCCCO1) `ZINC001520018632.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001520018632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001520018632 none CC(C)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 10, 10, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 34, 43, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 34, 27, 27, 15, 15, 3, 3, 3, 3, 3, 15, 15, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 579) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/579: 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)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@@H]1CCCCO1) `ZINC001520018632.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001520018632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001520018632 none CC(C)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 10, 10, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 34, 43, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 34, 27, 27, 15, 15, 3, 3, 3, 3, 3, 15, 15, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520018632 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 Building ZINC001520018632 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001520018632 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 576) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@@H]1CCCCO1) `ZINC001520018632.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520018632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001520018632 none CC(C)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 14, 9, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 33, 44, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 33, 33, 25, 25, 15, 15, 3, 3, 3, 3, 3, 15, 15, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 577) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@@H]1CCCCO1) `ZINC001520018632.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520018632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001520018632 none CC(C)N(Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 14, 9, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 33, 44, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 33, 33, 25, 25, 15, 15, 3, 3, 3, 3, 3, 15, 15, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 578) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/578: 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)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@@H]1CCCCO1) `ZINC001520018632.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001520018632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001520018632 none CC(C)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 10, 10, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 34, 43, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 34, 27, 27, 15, 15, 3, 3, 3, 3, 3, 15, 15, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 579) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/579: 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)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@@H]1CCCCO1) `ZINC001520018632.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001520018632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001520018632 none CC(C)N(Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)cc1)C[C@@H]1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 10, 10, 15, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 15, 15, 34, 43, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 34, 34, 27, 27, 15, 15, 3, 3, 3, 3, 3, 15, 15, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520018632 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520018632 Building ZINC001520128509 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520128509' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520128509 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520128509 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520128509/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520128509 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/580 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(COc2ccc(Cl)nc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001520128509.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520128509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520128509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001520128509 none O=C(N1CCC(COc2ccc(Cl)nc2)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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 8, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 4, 4, 4, 4, 10, 27, 49, 49, 49, 49, 49, 49, 4, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 10, 10, 49, 49, 49, 4, 4, 4, 4, 3, 3, 3] 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: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520128509 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520128509/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520128509 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 581) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/581 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/581' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(COc2ccc(Cl)nc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001520128509.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520128509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520128509/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001520128509 none O=C(N1CCC(COc2ccc(Cl)nc2)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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 8, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 4, 4, 4, 4, 14, 36, 49, 49, 49, 49, 49, 49, 4, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 4, 4, 4, 4, 14, 14, 49, 49, 49, 4, 4, 4, 4, 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, 38, 39, 40, 41, 42, 43]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520128509 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520128509 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520128509/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520128509/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520128509 Building ZINC001520128509 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520128509' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520128509 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520128509 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520128509/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520128509 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 580) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CCC(COc2ccc(Cl)nc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001520128509.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520128509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520128509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001520128509 none O=C(N1CCC(COc2ccc(Cl)nc2)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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 8, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 4, 4, 4, 4, 10, 27, 49, 49, 49, 49, 49, 49, 4, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 10, 10, 49, 49, 49, 4, 4, 4, 4, 3, 3, 3] 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: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520128509 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520128509/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520128509 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 581) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CCC(COc2ccc(Cl)nc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001520128509.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520128509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520128509/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001520128509 none O=C(N1CCC(COc2ccc(Cl)nc2)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', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 8, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 4, 4, 4, 4, 14, 36, 49, 49, 49, 49, 49, 49, 4, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 4, 4, 4, 4, 4, 14, 14, 49, 49, 49, 4, 4, 4, 4, 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, 38, 39, 40, 41, 42, 43]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520128509 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520128509 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520128509/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520128509/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520128509 Building ZINC001520199244 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520199244' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520199244 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520199244 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520199244/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520199244 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/582 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)(F)F)c(Br)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001520199244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520199244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520199244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001520199244 none O=C(Nc1ccc(OC(F)(F)F)c(Br)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'F', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 17, 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] 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, 7, 7, 7] 0 hydrogens need rotated 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, 12, 12, 12, 12, 27, 28, 28, 28, 12, 12, 12, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 12, 12, 12, 4, 4, 4, 4, 4, 4, 4, 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, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520199244 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520199244/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520199244 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 583) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/583 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/583' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)(F)F)c(Br)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001520199244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520199244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520199244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001520199244 none O=C(Nc1ccc(OC(F)(F)F)c(Br)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'F', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 17, 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] 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, 7, 7, 7] 0 hydrogens need rotated 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, 12, 12, 8, 12, 27, 28, 28, 28, 12, 12, 12, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 12, 12, 12, 4, 4, 4, 4, 4, 4, 4, 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, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520199244 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520199244 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520199244/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520199244/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520199244 Building ZINC001520199244 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520199244' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520199244 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520199244 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520199244/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520199244 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 582) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ccc(OC(F)(F)F)c(Br)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001520199244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520199244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520199244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001520199244 none O=C(Nc1ccc(OC(F)(F)F)c(Br)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'F', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 17, 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] 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, 7, 7, 7] 0 hydrogens need rotated 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, 12, 12, 12, 12, 27, 28, 28, 28, 12, 12, 12, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 12, 12, 12, 4, 4, 4, 4, 4, 4, 4, 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, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520199244 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520199244/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520199244 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 583) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ccc(OC(F)(F)F)c(Br)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001520199244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520199244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520199244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 42 natoms 41 natoms 40 natoms 39 names: ZINC001520199244 none O=C(Nc1ccc(OC(F)(F)F)c(Br)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', 'F', 'C.ar', 'Br', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 17, 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] 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, 7, 7, 7] 0 hydrogens need rotated 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, 12, 12, 8, 12, 27, 28, 28, 28, 12, 12, 12, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 12, 12, 12, 4, 4, 4, 4, 4, 4, 4, 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, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520199244 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520199244 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520199244/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520199244/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520199244 Building ZINC001520201797 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520201797' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520201797 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520201797 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520201797/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520201797 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/584 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCc2ccc(Oc3ccc(F)cc3)cc2)cc1Cl) `ZINC001520201797.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520201797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520201797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001520201797 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCc2ccc(Oc3ccc(F)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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 6, 6, 4, 4, 4, 6, 6, 6, 4, 4, 2, 4, 4, 6, 6, 6, 6, 26, 26, 26, 26, 6, 6, 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520201797 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520201797/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520201797 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 585) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/585 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/585' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCc2ccc(Oc3ccc(F)cc3)cc2)cc1Cl) `ZINC001520201797.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520201797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520201797/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001520201797 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCc2ccc(Oc3ccc(F)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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 6, 6, 4, 4, 4, 6, 6, 6, 4, 4, 2, 4, 4, 6, 6, 6, 6, 27, 27, 27, 27, 6, 6, 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520201797 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520201797 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520201797/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520201797/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520201797 Building ZINC001520201797 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520201797' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520201797 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520201797 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520201797/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520201797 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 584) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCc2ccc(Oc3ccc(F)cc3)cc2)cc1Cl) `ZINC001520201797.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520201797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520201797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001520201797 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCc2ccc(Oc3ccc(F)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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 6, 6, 4, 4, 4, 6, 6, 6, 4, 4, 2, 4, 4, 6, 6, 6, 6, 26, 26, 26, 26, 6, 6, 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520201797 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520201797/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520201797 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 585) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)NCCc2ccc(Oc3ccc(F)cc3)cc2)cc1Cl) `ZINC001520201797.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520201797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520201797/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001520201797 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCc2ccc(Oc3ccc(F)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', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 6, 6, 4, 4, 4, 6, 6, 6, 4, 4, 2, 4, 4, 6, 6, 6, 6, 27, 27, 27, 27, 6, 6, 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520201797 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520201797 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520201797/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520201797/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520201797 Building ZINC001520202173 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202173' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202173 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520202173 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202173/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202173 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/586 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/586' -> `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)ccc1Br) `ZINC001520202173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520202173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001520202173 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', '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, 16, 1, 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, 15, 15, 4, 15, 15, 4, 4, 1, 1, 1, 1, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 15, 15, 4, 15, 15, 4, 4, 4, 6, 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]) total number of confs: 75 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202173 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202173/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202173 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 587) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/587 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/587' -> `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)ccc1Br) `ZINC001520202173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520202173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001520202173 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', '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, 16, 1, 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, 15, 15, 4, 15, 15, 4, 4, 1, 1, 1, 1, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 4, 4, 4, 15, 15, 6, 15, 15, 4, 4, 4, 6, 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]) total number of confs: 78 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202173 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520202173 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202173/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202173/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202173 Building ZINC001520202173 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202173' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202173 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520202173 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202173/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202173 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 586) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1Br) `ZINC001520202173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520202173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001520202173 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', '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, 16, 1, 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, 15, 15, 4, 15, 15, 4, 4, 1, 1, 1, 1, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 15, 15, 4, 15, 15, 4, 4, 4, 6, 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]) total number of confs: 75 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202173 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202173/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202173 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 587) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1Br) `ZINC001520202173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520202173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001520202173 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', '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, 16, 1, 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, 15, 15, 4, 15, 15, 4, 4, 1, 1, 1, 1, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 4, 4, 4, 15, 15, 6, 15, 15, 4, 4, 4, 6, 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]) total number of confs: 78 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202173 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520202173 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202173/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202173/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202173 Building ZINC001520202198 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202198' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202198 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520202198 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202198/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202198 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/588 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1ccc(Oc2ccc(F)cc2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001520202198.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520202198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001520202198 none O=C(NCCc1ccc(Oc2ccc(F)cc2)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', 'O.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', '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, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 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] 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, 7, 11, 11, 11, 11, 11, 47, 50, 50, 50, 50, 50, 50, 11, 11, 1, 1, 1, 2, 2, 2, 2, 2, 2, 7, 7, 11, 11, 11, 11, 50, 50, 50, 50, 11, 11, 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: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202198 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202198/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202198 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 589) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/589 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/589' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1ccc(Oc2ccc(F)cc2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001520202198.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520202198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001520202198 none O=C(NCCc1ccc(Oc2ccc(F)cc2)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', 'O.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', '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, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 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] 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, 7, 11, 11, 11, 11, 11, 47, 50, 50, 47, 47, 50, 50, 11, 11, 1, 1, 1, 2, 2, 2, 2, 2, 2, 7, 7, 11, 11, 11, 11, 50, 50, 50, 50, 11, 11, 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: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202198 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520202198 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202198/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202198/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202198 Building ZINC001520202198 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202198' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202198 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520202198 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202198/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202198 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 588) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NCCc1ccc(Oc2ccc(F)cc2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001520202198.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520202198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001520202198 none O=C(NCCc1ccc(Oc2ccc(F)cc2)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', 'O.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', '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, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 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] 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, 7, 11, 11, 11, 11, 11, 47, 50, 50, 50, 50, 50, 50, 11, 11, 1, 1, 1, 2, 2, 2, 2, 2, 2, 7, 7, 11, 11, 11, 11, 50, 50, 50, 50, 11, 11, 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: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202198 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202198/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202198 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 589) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NCCc1ccc(Oc2ccc(F)cc2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001520202198.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520202198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001520202198 none O=C(NCCc1ccc(Oc2ccc(F)cc2)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', 'O.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', '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, 1, 1, 1, 1, 12, 1, 1, 1, 1, 15, 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] 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, 7, 11, 11, 11, 11, 11, 47, 50, 50, 47, 47, 50, 50, 11, 11, 1, 1, 1, 2, 2, 2, 2, 2, 2, 7, 7, 11, 11, 11, 11, 50, 50, 50, 50, 11, 11, 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: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202198 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520202198 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202198/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202198/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520202198 Building ZINC001520230753 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520230753' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520230753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520230753 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520230753/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520230753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/590 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1)c1cccs1) `ZINC001520230753.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520230753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520230753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001520230753 none O=C(Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1)c1cccs1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 14, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 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] 0 hydrogens 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, 5, 3, 11, 11, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 11, 11, 23, 34, 34, 34, 34, 19, 11, 11, 3, 9, 9, 11, 11, 34, 34, 34] 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520230753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520230753/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520230753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 591) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/591 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/591' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1)c1cccs1) `ZINC001520230753.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520230753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520230753/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001520230753 none O=C(Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1)c1cccs1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 14, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 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] 0 hydrogens 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, 21, 9, 5, 11, 11, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 11, 11, 22, 36, 36, 36, 36, 24, 11, 11, 3, 8, 8, 11, 11, 36, 36, 36] 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520230753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520230753 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520230753/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520230753/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520230753 Building ZINC001520230753 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520230753' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520230753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520230753 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520230753/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520230753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 590) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1)c1cccs1) `ZINC001520230753.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520230753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520230753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001520230753 none O=C(Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1)c1cccs1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 14, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 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] 0 hydrogens 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, 5, 3, 11, 11, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 11, 11, 23, 34, 34, 34, 34, 19, 11, 11, 3, 9, 9, 11, 11, 34, 34, 34] 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520230753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520230753/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520230753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 591) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1)c1cccs1) `ZINC001520230753.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520230753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520230753/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001520230753 none O=C(Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1)c1cccs1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 14, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 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] 0 hydrogens 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, 21, 9, 5, 11, 11, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 11, 11, 22, 36, 36, 36, 36, 24, 11, 11, 3, 8, 8, 11, 11, 36, 36, 36] 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520230753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520230753 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520230753/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520230753/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520230753 Building ZINC001520237120 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520237120' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520237120 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520237120 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520237120/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520237120 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/592 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1cc(Br)ccc1F)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001520237120.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520237120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520237120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520237120 none CCN(Cc1cc(Br)ccc1F)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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 17, 1, 1, 1, 15, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 6, 3, 6, 16, 24, 24, 24, 23, 24, 24, 24, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 16, 16, 24, 24, 24, 4, 4] 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520237120 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520237120/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520237120 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 593) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/593 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/593' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1cc(Br)ccc1F)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001520237120.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520237120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520237120/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520237120 none CCN(Cc1cc(Br)ccc1F)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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 17, 1, 1, 1, 15, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 6, 3, 6, 15, 24, 24, 24, 18, 24, 24, 24, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 15, 15, 24, 24, 24, 4, 4] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520237120 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520237120 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520237120/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520237120/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520237120 Building ZINC001520237120 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520237120' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520237120 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520237120 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520237120/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520237120 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 592) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCN(Cc1cc(Br)ccc1F)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001520237120.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520237120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520237120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520237120 none CCN(Cc1cc(Br)ccc1F)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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 17, 1, 1, 1, 15, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 6, 3, 6, 16, 24, 24, 24, 23, 24, 24, 24, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 16, 16, 24, 24, 24, 4, 4] 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520237120 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520237120/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520237120 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 593) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCN(Cc1cc(Br)ccc1F)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001520237120.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520237120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520237120/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520237120 none CCN(Cc1cc(Br)ccc1F)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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 17, 1, 1, 1, 15, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 6, 3, 6, 15, 24, 24, 24, 18, 24, 24, 24, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 15, 15, 24, 24, 24, 4, 4] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520237120 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520237120 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520237120/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520237120/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520237120 Building ZINC001520298140 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520298140' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520298140 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520298140 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520298140/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520298140 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/594 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCSCc2ccc(Cl)cc2Cl)cc1Cl) `ZINC001520298140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520298140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520298140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001520298140 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCSCc2ccc(Cl)cc2Cl)cc1Cl NO_LONG_NAME dock atom 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', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 1, 1, 1, 1, 16, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 5, 10, 22, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 9, 9, 9, 4, 4, 2, 4, 4, 5, 5, 22, 22, 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520298140 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520298140/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520298140 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 595) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/595 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/595' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCSCc2ccc(Cl)cc2Cl)cc1Cl) `ZINC001520298140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520298140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520298140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001520298140 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCSCc2ccc(Cl)cc2Cl)cc1Cl NO_LONG_NAME dock atom 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', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 1, 1, 1, 1, 16, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 5, 9, 21, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 9, 9, 9, 4, 4, 2, 4, 4, 5, 5, 21, 21, 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520298140 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520298140 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520298140/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520298140/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520298140 Building ZINC001520298140 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520298140' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520298140 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520298140 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520298140/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520298140 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 594) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCSCc2ccc(Cl)cc2Cl)cc1Cl) `ZINC001520298140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520298140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520298140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001520298140 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCSCc2ccc(Cl)cc2Cl)cc1Cl NO_LONG_NAME dock atom 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', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 1, 1, 1, 1, 16, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 5, 10, 22, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 9, 9, 9, 4, 4, 2, 4, 4, 5, 5, 22, 22, 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520298140 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520298140/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520298140 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 595) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)NCCSCc2ccc(Cl)cc2Cl)cc1Cl) `ZINC001520298140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520298140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520298140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001520298140 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCSCc2ccc(Cl)cc2Cl)cc1Cl NO_LONG_NAME dock atom 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', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 1, 1, 1, 1, 16, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 5, 9, 21, 26, 26, 26, 26, 26, 26, 26, 4, 4, 4, 9, 9, 9, 4, 4, 2, 4, 4, 5, 5, 21, 21, 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520298140 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520298140 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520298140/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520298140/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520298140 Building ZINC001520301585 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520301585' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520301585 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520301585 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520301585/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520301585 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/596 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)F)c(C(F)(F)F)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001520301585.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520301585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520301585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001520301585 none O=C(Nc1ccc(OC(F)F)c(C(F)(F)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', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.3', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 5, 15, 15, 15, 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, 11, 11, 8, 7, 22, 37, 37, 11, 11, 11, 11, 11, 11, 1, 1, 1, 6, 6, 6, 6, 6, 2, 11, 11, 37, 11, 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520301585 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520301585/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520301585 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 597) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/597 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/597' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OC(F)F)c(C(F)(F)F)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001520301585.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520301585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520301585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001520301585 none O=C(Nc1ccc(OC(F)F)c(C(F)(F)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', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.3', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 5, 15, 15, 15, 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, 11, 11, 4, 8, 23, 37, 37, 11, 11, 11, 11, 11, 11, 1, 1, 1, 6, 6, 6, 6, 6, 2, 11, 11, 37, 11, 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520301585 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520301585 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520301585/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520301585/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520301585 Building ZINC001520301585 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520301585' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520301585 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520301585 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520301585/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520301585 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 596) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ccc(OC(F)F)c(C(F)(F)F)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001520301585.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520301585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520301585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001520301585 none O=C(Nc1ccc(OC(F)F)c(C(F)(F)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', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.3', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 5, 15, 15, 15, 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, 11, 11, 8, 7, 22, 37, 37, 11, 11, 11, 11, 11, 11, 1, 1, 1, 6, 6, 6, 6, 6, 2, 11, 11, 37, 11, 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520301585 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520301585/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520301585 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 597) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ccc(OC(F)F)c(C(F)(F)F)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001520301585.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520301585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520301585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001520301585 none O=C(Nc1ccc(OC(F)F)c(C(F)(F)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', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.3', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 15, 15, 1, 5, 15, 15, 15, 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, 11, 11, 4, 8, 23, 37, 37, 11, 11, 11, 11, 11, 11, 1, 1, 1, 6, 6, 6, 6, 6, 2, 11, 11, 37, 11, 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520301585 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520301585 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520301585/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520301585/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520301585 Building ZINC001520370872 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520370872' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520370872 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520370872 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520370872/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520370872 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/598 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1cccc(Cl)c1) `ZINC001520370872.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520370872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520370872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520370872 none CCc1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1cccc(Cl)c1 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.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', '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: [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, 16, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 4, 4, 4, 4, 23, 23, 23, 23, 23, 23, 8, 8, 8, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 4, 23, 23, 23, 23] 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]) total number of confs: 61 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520370872 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520370872/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520370872 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 599) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/599 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/599' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1cccc(Cl)c1) `ZINC001520370872.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520370872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520370872/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520370872 none CCc1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1cccc(Cl)c1 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.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', '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: [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, 16, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 3, 4, 4, 2, 2, 4, 4, 4, 4, 23, 23, 9, 23, 23, 23, 8, 8, 8, 8, 8, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 4, 23, 23, 23, 23] 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]) total number of confs: 114 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520370872 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520370872 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520370872/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520370872/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520370872 Building ZINC001520370872 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520370872' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520370872 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520370872 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520370872/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520370872 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 598) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCc1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1cccc(Cl)c1) `ZINC001520370872.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520370872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520370872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520370872 none CCc1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1cccc(Cl)c1 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.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', '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: [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, 16, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 4, 4, 4, 4, 23, 23, 23, 23, 23, 23, 8, 8, 8, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 4, 23, 23, 23, 23] 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]) total number of confs: 61 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520370872 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520370872/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520370872 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 599) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCc1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1cccc(Cl)c1) `ZINC001520370872.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520370872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520370872/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520370872 none CCc1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cnn1c1cccc(Cl)c1 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.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', '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: [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, 16, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 3, 4, 4, 2, 2, 4, 4, 4, 4, 23, 23, 9, 23, 23, 23, 8, 8, 8, 8, 8, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 4, 23, 23, 23, 23] 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]) total number of confs: 114 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520370872 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520370872 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520370872/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520370872/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520370872 Building ZINC001520397103 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520397103' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520397103 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520397103 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520397103/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520397103 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/600 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/600' -> `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])c1ccc(Cl)cc1) `ZINC001520397103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520397103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520397103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520397103 none O=C(Nc1c(Br)cc(F)cc1Br)[C@]([O-])([SiH3])c1ccc(Cl)cc1 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', 'Cl', 'C.ar', 'C.ar', '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, 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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 10, 18, 18, 18, 10, 11, 18, 18, 18, 1, 1, 1, 6, 6, 1, 1, 6, 6, 10, 18, 18, 6, 6, 6, 6] 21 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: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520397103 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520397103/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520397103 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 601) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/601 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/601' -> `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])c1ccc(Cl)cc1) `ZINC001520397103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520397103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520397103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520397103 none O=C(Nc1c(Br)cc(F)cc1Br)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 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', 'Cl', 'C.ar', 'C.ar', '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, 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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 10, 18, 18, 18, 10, 13, 18, 18, 18, 1, 1, 1, 6, 6, 1, 1, 6, 6, 10, 18, 18, 6, 6, 6, 6] 21 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/12845/xbi-8058088.35/working/building/ZINC001520397103 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520397103 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520397103/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520397103/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520397103 Building ZINC001520397103 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520397103' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520397103 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520397103 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520397103/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520397103 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 600) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(Nc1c(Br)cc(F)cc1Br)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001520397103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520397103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520397103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520397103 none O=C(Nc1c(Br)cc(F)cc1Br)[C@]([O-])([SiH3])c1ccc(Cl)cc1 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', 'Cl', 'C.ar', 'C.ar', '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, 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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 10, 18, 18, 18, 10, 11, 18, 18, 18, 1, 1, 1, 6, 6, 1, 1, 6, 6, 10, 18, 18, 6, 6, 6, 6] 21 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: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520397103 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520397103/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520397103 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 601) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(Nc1c(Br)cc(F)cc1Br)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001520397103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520397103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520397103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520397103 none O=C(Nc1c(Br)cc(F)cc1Br)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 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', 'Cl', 'C.ar', 'C.ar', '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, 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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 10, 18, 18, 18, 10, 13, 18, 18, 18, 1, 1, 1, 6, 6, 1, 1, 6, 6, 10, 18, 18, 6, 6, 6, 6] 21 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/12845/xbi-8058088.35/working/building/ZINC001520397103 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520397103 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520397103/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520397103/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520397103 Building ZINC001520426322 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520426322' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520426322 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520426322 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520426322/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520426322 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/602 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc2c1CN(C(=O)OC(C)(C)C)CCN2C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001520426322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520426322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520426322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520426322 none Cc1cccc2c1CN(C(=O)OC(C)(C)C)CCN2C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 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.2', 'O.2', 'O.3', 'C.3', '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', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 32, 32, 50, 50, 50, 50, 17, 17, 12, 3, 13, 1, 1, 1, 2, 2, 1, 1, 2, 2, 17, 17, 17, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 2, 2, 2] 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: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520426322 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520426322/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520426322 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 603) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/603 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/603' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc2c1CN(C(=O)OC(C)(C)C)CCN2C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001520426322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520426322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520426322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520426322 none Cc1cccc2c1CN(C(=O)OC(C)(C)C)CCN2C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 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.2', 'O.2', 'O.3', 'C.3', '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', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 33, 33, 50, 50, 50, 50, 17, 17, 12, 3, 13, 1, 1, 1, 2, 2, 1, 1, 2, 2, 17, 17, 17, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 2, 2, 2] 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520426322 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520426322 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520426322/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520426322/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520426322 Building ZINC001520426322 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520426322' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520426322 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520426322 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520426322/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520426322 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 602) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1cccc2c1CN(C(=O)OC(C)(C)C)CCN2C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001520426322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520426322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520426322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520426322 none Cc1cccc2c1CN(C(=O)OC(C)(C)C)CCN2C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 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.2', 'O.2', 'O.3', 'C.3', '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', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 32, 32, 50, 50, 50, 50, 17, 17, 12, 3, 13, 1, 1, 1, 2, 2, 1, 1, 2, 2, 17, 17, 17, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 2, 2, 2] 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: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520426322 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520426322/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520426322 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 603) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1cccc2c1CN(C(=O)OC(C)(C)C)CCN2C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001520426322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520426322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520426322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520426322 none Cc1cccc2c1CN(C(=O)OC(C)(C)C)CCN2C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 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.2', 'O.2', 'O.3', 'C.3', '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', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 33, 33, 50, 50, 50, 50, 17, 17, 12, 3, 13, 1, 1, 1, 2, 2, 1, 1, 2, 2, 17, 17, 17, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 2, 2, 2] 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: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520426322 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520426322 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520426322/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520426322/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520426322 Building ZINC001520450613 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520450613' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520450613 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520450613 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520450613/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520450613 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/604 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnc2c(Cl)cc(Br)cc12)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001520450613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520450613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520450613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001520450613 none O=C(Nc1ccnc2c(Cl)cc(Br)cc12)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 1, 1, 16, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 5, 20, 20, 20, 20, 10, 10, 10, 10, 10, 10, 10, 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, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520450613 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520450613/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520450613 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 605) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/605 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/605' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnc2c(Cl)cc(Br)cc12)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001520450613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520450613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520450613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001520450613 none O=C(Nc1ccnc2c(Cl)cc(Br)cc12)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 1, 1, 16, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 5, 20, 20, 20, 20, 10, 10, 10, 10, 10, 10, 10, 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, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520450613 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520450613 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520450613/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520450613/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520450613 Building ZINC001520450613 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520450613' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520450613 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520450613 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520450613/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520450613 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 604) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ccnc2c(Cl)cc(Br)cc12)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001520450613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520450613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520450613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001520450613 none O=C(Nc1ccnc2c(Cl)cc(Br)cc12)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 1, 1, 16, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 5, 20, 20, 20, 20, 10, 10, 10, 10, 10, 10, 10, 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, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520450613 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520450613/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520450613 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 605) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ccnc2c(Cl)cc(Br)cc12)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001520450613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520450613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520450613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001520450613 none O=C(Nc1ccnc2c(Cl)cc(Br)cc12)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 1, 1, 16, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 5, 20, 20, 20, 20, 10, 10, 10, 10, 10, 10, 10, 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, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520450613 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520450613 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520450613/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520450613/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520450613 Building ZINC001520507054 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507054' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507054 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520507054 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507054/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507054 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/606 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(COc2ccc(C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)cc1) `ZINC001520507054.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520507054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001520507054 none Cc1ccc(COc2ccc(C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 18, 18, 18, 11, 18, 18, 11, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 28, 28, 28, 28, 28, 28, 28, 18, 18, 18, 18, 11, 11, 6, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 28, 28] 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, 58, 59, 60]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507054 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507054/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507054 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 607) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/607 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/607' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(COc2ccc(C[C@H](C)NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)cc1) `ZINC001520507054.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520507054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001520507054 none Cc1ccc(COc2ccc(C[C@H](C)NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 11, 16, 16, 11, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 25, 25, 25, 25, 25, 25, 25, 16, 16, 16, 16, 11, 11, 6, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 25, 25] 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, 58, 59, 60]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507054 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520507054 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507054/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507054/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507054 Building ZINC001520507054 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507054' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507054 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520507054 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507054/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507054 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 606) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc(COc2ccc(C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)cc1) `ZINC001520507054.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520507054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001520507054 none Cc1ccc(COc2ccc(C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 18, 18, 18, 11, 18, 18, 11, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 28, 28, 28, 28, 28, 28, 28, 18, 18, 18, 18, 11, 11, 6, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 28, 28] 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, 58, 59, 60]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507054 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507054/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507054 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 607) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc(COc2ccc(C[C@H](C)NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)cc1) `ZINC001520507054.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520507054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001520507054 none Cc1ccc(COc2ccc(C[C@H](C)NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 11, 16, 16, 11, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 25, 25, 25, 25, 25, 25, 25, 16, 16, 16, 16, 11, 11, 6, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 25, 25] 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, 58, 59, 60]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507054 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520507054 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507054/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507054/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507054 Building ZINC001520507057 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507057' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507057 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520507057 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507057/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507057 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/608 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(COc2ccc(C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)cc1) `ZINC001520507057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520507057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001520507057 none Cc1ccc(COc2ccc(C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 16, 16, 11, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 25, 25, 25, 25, 25, 25, 25, 16, 16, 16, 16, 11, 11, 6, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 25, 25] 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, 58, 59, 60]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507057 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507057/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507057 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 609) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/609 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/609' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(COc2ccc(C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)cc1) `ZINC001520507057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520507057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001520507057 none Cc1ccc(COc2ccc(C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 17, 11, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 27, 27, 27, 27, 27, 27, 27, 17, 17, 17, 17, 11, 11, 6, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 27, 27] 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, 58, 59, 60]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507057 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520507057 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507057/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507057/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507057 Building ZINC001520507057 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507057' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507057 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520507057 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507057/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507057 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 608) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc(COc2ccc(C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)cc1) `ZINC001520507057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520507057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001520507057 none Cc1ccc(COc2ccc(C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 16, 16, 11, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 25, 25, 25, 25, 25, 25, 25, 16, 16, 16, 16, 11, 11, 6, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 25, 25] 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, 58, 59, 60]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507057 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507057/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507057 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 609) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc(COc2ccc(C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)cc1) `ZINC001520507057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520507057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC001520507057 none Cc1ccc(COc2ccc(C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', '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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 17, 17, 11, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 27, 27, 27, 27, 27, 27, 27, 17, 17, 17, 17, 11, 11, 6, 6, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 17, 17, 27, 27] 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, 58, 59, 60]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507057 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520507057 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507057/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507057/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520507057 Building ZINC001520513928 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520513928' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520513928 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520513928 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520513928/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520513928 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/610 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c2ccccc2nc1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001520513928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520513928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520513928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001520513928 none Cn1c2ccccc2nc1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', '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', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 36, 36, 21, 16, 21, 21, 5, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 21, 21, 36, 36, 36, 36, 36, 36, 36, 21, 21, 5, 11, 11, 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520513928 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520513928/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520513928 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 611) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/611 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/611' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c2ccccc2nc1c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001520513928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520513928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520513928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001520513928 none Cn1c2ccccc2nc1c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', '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', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 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, 6, 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] 0 hydrogens 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, 35, 35, 35, 35, 35, 35, 6, 6, 22, 22, 6, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 22, 22, 35, 35, 35, 35, 35, 35, 35, 22, 22, 6, 11, 11, 22, 22] 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520513928 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520513928 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520513928/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520513928/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520513928 Building ZINC001520513928 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520513928' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520513928 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520513928 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520513928/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520513928 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 610) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cn1c2ccccc2nc1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001520513928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520513928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520513928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001520513928 none Cn1c2ccccc2nc1c1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', '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', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 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, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 36, 36, 21, 16, 21, 21, 5, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 21, 21, 36, 36, 36, 36, 36, 36, 36, 21, 21, 5, 11, 11, 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520513928 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520513928/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520513928 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 611) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cn1c2ccccc2nc1c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001520513928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520513928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520513928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001520513928 none Cn1c2ccccc2nc1c1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', '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', '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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 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, 6, 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] 0 hydrogens 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, 35, 35, 35, 35, 35, 35, 6, 6, 22, 22, 6, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 22, 22, 35, 35, 35, 35, 35, 35, 35, 22, 22, 6, 11, 11, 22, 22] 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520513928 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520513928 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520513928/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520513928/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520513928 Building ZINC001520532234 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532234' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532234 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520532234 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532234/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532234 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/612 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)c2ccc(C(F)(F)F)cc2)cc1) `ZINC001520532234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520532234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520532234 none COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)c2ccc(C(F)(F)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 10, 36, 36, 10, 6, 10, 6, 1, 6, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 10, 31, 31, 10, 10, 31, 31, 31, 31, 31, 36, 36, 36, 36, 36, 36, 36, 6, 3, 3, 3, 3, 3, 3, 3, 31, 31, 31, 31, 36, 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, 48, 49, 50, 51]) total number of confs: 310 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532234 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532234/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532234 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 613) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/613 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/613' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)c2ccc(C(F)(F)F)cc2)cc1) `ZINC001520532234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520532234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520532234 none COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)c2ccc(C(F)(F)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 35, 35, 12, 6, 12, 6, 1, 6, 1, 1, 1, 4, 4, 3, 4, 4, 4, 4, 12, 30, 30, 12, 12, 30, 30, 30, 30, 30, 35, 35, 35, 35, 35, 35, 35, 6, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 35, 35] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 291 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532234 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520532234 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532234/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532234/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532234 Building ZINC001520532234 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532234' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532234 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520532234 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532234/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532234 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 612) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)c2ccc(C(F)(F)F)cc2)cc1) `ZINC001520532234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520532234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520532234 none COc1ccc([C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)c2ccc(C(F)(F)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 10, 36, 36, 10, 6, 10, 6, 1, 6, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 10, 31, 31, 10, 10, 31, 31, 31, 31, 31, 36, 36, 36, 36, 36, 36, 36, 6, 3, 3, 3, 3, 3, 3, 3, 31, 31, 31, 31, 36, 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, 48, 49, 50, 51]) total number of confs: 310 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532234 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532234/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532234 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 613) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)c2ccc(C(F)(F)F)cc2)cc1) `ZINC001520532234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520532234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520532234 none COc1ccc([C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)c2ccc(C(F)(F)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 35, 35, 12, 6, 12, 6, 1, 6, 1, 1, 1, 4, 4, 3, 4, 4, 4, 4, 12, 30, 30, 12, 12, 30, 30, 30, 30, 30, 35, 35, 35, 35, 35, 35, 35, 6, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 35, 35] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 291 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532234 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520532234 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532234/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532234/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532234 Building ZINC001520532236 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532236' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532236 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520532236 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532236/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532236 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/614 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)c2ccc(C(F)(F)F)cc2)cc1) `ZINC001520532236.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520532236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520532236 none COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)c2ccc(C(F)(F)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 33, 33, 11, 6, 11, 6, 1, 6, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 11, 29, 29, 29, 29, 29, 29, 29, 29, 29, 33, 33, 33, 33, 33, 33, 33, 6, 3, 3, 3, 3, 3, 3, 3, 29, 29, 29, 29, 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]) total number of confs: 174 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532236 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532236/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532236 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 615) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/615 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/615' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)c2ccc(C(F)(F)F)cc2)cc1) `ZINC001520532236.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520532236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532236/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520532236 none COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)c2ccc(C(F)(F)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 17, 36, 36, 12, 6, 12, 6, 1, 6, 1, 1, 1, 4, 4, 3, 4, 4, 4, 4, 12, 30, 30, 16, 19, 30, 30, 30, 30, 30, 36, 36, 36, 36, 36, 36, 36, 6, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 36, 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, 48, 49, 50, 51]) total number of confs: 268 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532236 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520532236 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532236/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532236/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532236 Building ZINC001520532236 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532236' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532236 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520532236 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532236/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532236 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 614) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)c2ccc(C(F)(F)F)cc2)cc1) `ZINC001520532236.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520532236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520532236 none COc1ccc([C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)c2ccc(C(F)(F)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 33, 33, 11, 6, 11, 6, 1, 6, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 11, 29, 29, 29, 29, 29, 29, 29, 29, 29, 33, 33, 33, 33, 33, 33, 33, 6, 3, 3, 3, 3, 3, 3, 3, 29, 29, 29, 29, 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]) total number of confs: 174 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532236 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532236/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532236 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 615) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)c2ccc(C(F)(F)F)cc2)cc1) `ZINC001520532236.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520532236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532236/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520532236 none COc1ccc([C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)c2ccc(C(F)(F)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 17, 36, 36, 12, 6, 12, 6, 1, 6, 1, 1, 1, 4, 4, 3, 4, 4, 4, 4, 12, 30, 30, 16, 19, 30, 30, 30, 30, 30, 36, 36, 36, 36, 36, 36, 36, 6, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 36, 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, 48, 49, 50, 51]) total number of confs: 268 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532236 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520532236 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532236/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532236/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520532236 Building ZINC001520650542 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520650542' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520650542 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520650542 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520650542/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520650542 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/616 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/616' -> `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)Nc1ncccc1OCC1CCCCC1) `ZINC001520650542.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520650542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520650542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001520650542 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ncccc1OCC1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 13, 31, 50, 50, 50, 50, 50, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 5, 5, 5, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520650542 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520650542/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520650542 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 617) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/617 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/617' -> `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)Nc1ncccc1OCC1CCCCC1) `ZINC001520650542.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520650542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520650542/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001520650542 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ncccc1OCC1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 14, 32, 50, 50, 50, 50, 50, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 2, 2, 5, 5, 5, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520650542 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520650542 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520650542/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520650542/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520650542 Building ZINC001520650542 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520650542' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520650542 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520650542 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520650542/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520650542 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 616) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/616: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ncccc1OCC1CCCCC1) `ZINC001520650542.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520650542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520650542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001520650542 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ncccc1OCC1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 13, 31, 50, 50, 50, 50, 50, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 2, 2, 5, 5, 5, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520650542 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520650542/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520650542 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 617) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/617: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ncccc1OCC1CCCCC1) `ZINC001520650542.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520650542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520650542/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001520650542 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ncccc1OCC1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 14, 32, 50, 50, 50, 50, 50, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 2, 2, 5, 5, 5, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520650542 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520650542 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520650542/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520650542/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520650542 Building ZINC001520669308 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520669308' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520669308 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520669308 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520669308/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520669308 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/618 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCCOc1c(Cl)cc(Br)cc1Cl) `ZINC001520669308.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520669308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520669308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001520669308 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCCOc1c(Cl)cc(Br)cc1Cl 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', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', '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, 12, 1, 1, 16, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 23, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 23, 23, 33, 33, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520669308 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520669308/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520669308 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 619) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/619 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/619' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCCOc1c(Cl)cc(Br)cc1Cl) `ZINC001520669308.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520669308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520669308/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001520669308 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCCOc1c(Cl)cc(Br)cc1Cl 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', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', '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, 12, 1, 1, 16, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 23, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 23, 23, 33, 33, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520669308 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520669308 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520669308/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520669308/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520669308 Building ZINC001520669308 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520669308' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520669308 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520669308 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520669308/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520669308 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 618) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCCOc1c(Cl)cc(Br)cc1Cl) `ZINC001520669308.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520669308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520669308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001520669308 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCCOc1c(Cl)cc(Br)cc1Cl 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', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', '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, 12, 1, 1, 16, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 23, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 23, 23, 33, 33, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520669308 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520669308/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520669308 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 619) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCCOc1c(Cl)cc(Br)cc1Cl) `ZINC001520669308.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520669308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520669308/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001520669308 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCCOc1c(Cl)cc(Br)cc1Cl 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', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', '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, 12, 1, 1, 16, 1, 1, 17, 1, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 23, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 23, 23, 33, 33, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520669308 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520669308 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520669308/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520669308/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520669308 Building ZINC001520704307 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520704307' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520704307 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520704307 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520704307/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520704307 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/620 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(CCC(C)C)c2nnc(C)c3ccccc32)cc1Cl) `ZINC001520704307.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520704307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520704307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001520704307 none COc1ccc([C@]([O-])([SiH3])C(=O)N(CCC(C)C)c2nnc(C)c3ccccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 6, 6, 1, 1, 1, 1, 2, 2, 5, 8, 8, 11, 12, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 10, 10, 10, 6, 6, 8, 8, 8, 8, 12, 11, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 90 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520704307 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520704307/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520704307 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 621) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/621 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/621' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(CCC(C)C)c2nnc(C)c3ccccc32)cc1Cl) `ZINC001520704307.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520704307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520704307/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001520704307 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(CCC(C)C)c2nnc(C)c3ccccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 5, 8, 8, 10, 12, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 9, 9, 9, 6, 6, 8, 8, 8, 8, 12, 10, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 94 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520704307 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520704307 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520704307/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520704307/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520704307 Building ZINC001520704307 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520704307' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520704307 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520704307 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520704307/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520704307 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 620) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)N(CCC(C)C)c2nnc(C)c3ccccc32)cc1Cl) `ZINC001520704307.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520704307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520704307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001520704307 none COc1ccc([C@]([O-])([SiH3])C(=O)N(CCC(C)C)c2nnc(C)c3ccccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 6, 6, 1, 1, 1, 1, 2, 2, 5, 8, 8, 11, 12, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 10, 10, 10, 6, 6, 8, 8, 8, 8, 12, 11, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 90 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520704307 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520704307/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520704307 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 621) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N(CCC(C)C)c2nnc(C)c3ccccc32)cc1Cl) `ZINC001520704307.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520704307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520704307/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001520704307 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(CCC(C)C)c2nnc(C)c3ccccc32)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 5, 8, 8, 10, 12, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 9, 9, 9, 6, 6, 8, 8, 8, 8, 12, 10, 12, 12, 12, 12, 12, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 94 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520704307 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520704307 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520704307/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520704307/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520704307 Building ZINC001520707720 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520707720' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520707720 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520707720 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520707720/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520707720 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/622 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2c(cccc2Br)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001520707720.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520707720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520707720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC001520707720 none O=C(Nc1nc2c(cccc2Br)s1)[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', 'Br', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens 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, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 12, 12, 12, 12, 12, 11, 20, 20, 20, 12, 12] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520707720 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520707720/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520707720 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 623) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/623 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/623' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2c(cccc2Br)s1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001520707720.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520707720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520707720/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC001520707720 none O=C(Nc1nc2c(cccc2Br)s1)[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', 'Br', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens 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, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 12, 12, 12, 12, 12, 11, 20, 20, 20, 12, 12] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520707720 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520707720 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520707720/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520707720/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520707720 Building ZINC001520707720 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520707720' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520707720 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520707720 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520707720/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520707720 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 622) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1nc2c(cccc2Br)s1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001520707720.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520707720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520707720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC001520707720 none O=C(Nc1nc2c(cccc2Br)s1)[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', 'Br', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens 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, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 12, 12, 12, 12, 12, 11, 20, 20, 20, 12, 12] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520707720 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520707720/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520707720 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 623) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1nc2c(cccc2Br)s1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001520707720.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520707720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520707720/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC001520707720 none O=C(Nc1nc2c(cccc2Br)s1)[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', 'Br', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 14, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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] 0 hydrogens 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, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 12, 12, 12, 12, 12, 11, 20, 20, 20, 12, 12] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520707720 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520707720 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520707720/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520707720/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520707720 Building ZINC001520719827 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520719827' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520719827 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520719827 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520719827/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520719827 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/624 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(c2ccc3c(c2)CCO3)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001520719827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520719827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520719827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520719827 none O=C(Nc1cccc(c2ccc3c(c2)CCO3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', '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, 1, 1, 1, 1, 1, 5, 5, 12, 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, 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] 0 hydrogens need rotated 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, 11, 11, 11, 11, 35, 35, 35, 35, 35, 35, 35, 35, 11, 1, 1, 1, 5, 5, 5, 5, 5, 2, 11, 11, 11, 35, 35, 35, 35, 35, 35, 35, 11, 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520719827 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520719827/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520719827 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 625) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/625 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/625' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(c2ccc3c(c2)CCO3)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001520719827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520719827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520719827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520719827 none O=C(Nc1cccc(c2ccc3c(c2)CCO3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', '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, 1, 1, 1, 1, 1, 5, 5, 12, 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, 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] 0 hydrogens need 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, 12, 12, 12, 12, 12, 36, 36, 36, 36, 36, 36, 36, 36, 12, 1, 1, 1, 4, 4, 4, 4, 4, 3, 12, 12, 12, 36, 36, 36, 36, 36, 36, 36, 12, 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: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520719827 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520719827 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520719827/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520719827/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520719827 Building ZINC001520719827 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520719827' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520719827 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520719827 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520719827/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520719827 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 624) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(Nc1cccc(c2ccc3c(c2)CCO3)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001520719827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520719827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520719827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520719827 none O=C(Nc1cccc(c2ccc3c(c2)CCO3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', '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, 1, 1, 1, 1, 1, 5, 5, 12, 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, 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] 0 hydrogens need rotated 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, 11, 11, 11, 11, 35, 35, 35, 35, 35, 35, 35, 35, 11, 1, 1, 1, 5, 5, 5, 5, 5, 2, 11, 11, 11, 35, 35, 35, 35, 35, 35, 35, 11, 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520719827 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520719827/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520719827 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 625) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(Nc1cccc(c2ccc3c(c2)CCO3)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001520719827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520719827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520719827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520719827 none O=C(Nc1cccc(c2ccc3c(c2)CCO3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', '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, 1, 1, 1, 1, 1, 5, 5, 12, 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, 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] 0 hydrogens need 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, 12, 12, 12, 12, 12, 36, 36, 36, 36, 36, 36, 36, 36, 12, 1, 1, 1, 4, 4, 4, 4, 4, 3, 12, 12, 12, 36, 36, 36, 36, 36, 36, 36, 12, 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: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520719827 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520719827 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520719827/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520719827/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520719827 Building ZINC001520756597 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756597' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756597 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520756597 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756597/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756597 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/626 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H](c2cc3cc(Br)cc(C)c3o2)C(C)C)cn1) `ZINC001520756597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520756597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001520756597 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H](c2cc3cc(Br)cc(C)c3o2)C(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.3', 'C.3', 'H', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 17, 1, 1, 5, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 5, 5, 1, 1, 1, 1, 2, 2, 5, 5, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 9, 9, 5, 5, 16, 16, 16, 16, 16, 5, 5, 5, 5, 18, 18, 18, 18, 18, 18, 9, 9, 9, 9, 9, 9, 9, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756597 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756597/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756597 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 627) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/627 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/627' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@@H](c2cc3cc(Br)cc(C)c3o2)C(C)C)cn1) `ZINC001520756597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520756597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001520756597 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@@H](c2cc3cc(Br)cc(C)c3o2)C(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.3', 'C.3', 'H', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 17, 1, 1, 5, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 2, 5, 5, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 15, 15, 5, 5, 18, 18, 18, 18, 18, 5, 5, 5, 5, 21, 21, 21, 21, 21, 21, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756597 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520756597 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756597/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756597/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756597 Building ZINC001520756597 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756597' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756597 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520756597 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756597/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756597 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 626) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H](c2cc3cc(Br)cc(C)c3o2)C(C)C)cn1) `ZINC001520756597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520756597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001520756597 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H](c2cc3cc(Br)cc(C)c3o2)C(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.3', 'C.3', 'H', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 17, 1, 1, 5, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 5, 5, 1, 1, 1, 1, 2, 2, 5, 5, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 9, 9, 5, 5, 16, 16, 16, 16, 16, 5, 5, 5, 5, 18, 18, 18, 18, 18, 18, 9, 9, 9, 9, 9, 9, 9, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756597 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756597/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756597 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 627) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@@H](c2cc3cc(Br)cc(C)c3o2)C(C)C)cn1) `ZINC001520756597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520756597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001520756597 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@@H](c2cc3cc(Br)cc(C)c3o2)C(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.3', 'C.3', 'H', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 17, 1, 1, 5, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 2, 5, 5, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 15, 15, 5, 5, 18, 18, 18, 18, 18, 5, 5, 5, 5, 21, 21, 21, 21, 21, 21, 15, 15, 15, 15, 15, 15, 15, 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]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756597 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520756597 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756597/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756597/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756597 Building ZINC001520756598 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756598' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756598 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520756598 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756598/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756598 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/628 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@H](c2cc3cc(Br)cc(C)c3o2)C(C)C)cn1) `ZINC001520756598.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520756598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001520756598 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@H](c2cc3cc(Br)cc(C)c3o2)C(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.3', 'C.3', 'H', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 17, 1, 1, 5, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 2, 5, 5, 10, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 10, 16, 16, 5, 5, 17, 17, 17, 17, 17, 5, 5, 5, 5, 22, 22, 22, 22, 22, 22, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 140 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756598 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756598/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756598 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 629) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/629 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/629' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@H](c2cc3cc(Br)cc(C)c3o2)C(C)C)cn1) `ZINC001520756598.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520756598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756598/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001520756598 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@H](c2cc3cc(Br)cc(C)c3o2)C(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.3', 'C.3', 'H', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 17, 1, 1, 5, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 5, 5, 1, 1, 1, 1, 2, 2, 5, 5, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 9, 9, 5, 5, 16, 16, 16, 16, 16, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 9, 9, 9, 9, 9, 9, 9, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756598 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520756598 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756598/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756598/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756598 Building ZINC001520756598 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756598' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756598 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520756598 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756598/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756598 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 628) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@H](c2cc3cc(Br)cc(C)c3o2)C(C)C)cn1) `ZINC001520756598.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520756598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001520756598 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@H](c2cc3cc(Br)cc(C)c3o2)C(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.3', 'C.3', 'H', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 17, 1, 1, 5, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 2, 5, 5, 10, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 10, 16, 16, 5, 5, 17, 17, 17, 17, 17, 5, 5, 5, 5, 22, 22, 22, 22, 22, 22, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 140 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756598 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756598/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756598 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 629) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@H](c2cc3cc(Br)cc(C)c3o2)C(C)C)cn1) `ZINC001520756598.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520756598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756598/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001520756598 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@H](c2cc3cc(Br)cc(C)c3o2)C(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.3', 'C.3', 'H', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 17, 1, 1, 5, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 5, 5, 1, 1, 1, 1, 2, 2, 5, 5, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 9, 9, 5, 5, 16, 16, 16, 16, 16, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 9, 9, 9, 9, 9, 9, 9, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756598 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520756598 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756598/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756598/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520756598 Building ZINC001520792408 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520792408' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520792408 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520792408 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520792408/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520792408 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/630 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccccc1OCc1ccccc1) `ZINC001520792408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520792408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520792408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001520792408 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccccc1OCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 8, 8, 5, 8, 8, 8, 13, 27, 35, 35, 30, 35, 35, 4, 4, 4, 2, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 27, 27, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520792408 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520792408/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520792408 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 631) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/631 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/631' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccccc1OCc1ccccc1) `ZINC001520792408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520792408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520792408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001520792408 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccccc1OCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 5, 5, 4, 5, 5, 5, 10, 27, 35, 35, 33, 35, 35, 4, 4, 4, 2, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 27, 27, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520792408 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520792408 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520792408/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520792408/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520792408 Building ZINC001520792408 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520792408' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520792408 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520792408 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520792408/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520792408 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 630) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccccc1OCc1ccccc1) `ZINC001520792408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520792408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520792408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001520792408 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccccc1OCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 8, 8, 5, 8, 8, 8, 13, 27, 35, 35, 30, 35, 35, 4, 4, 4, 2, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 27, 27, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520792408 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520792408/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520792408 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 631) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccccc1OCc1ccccc1) `ZINC001520792408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520792408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520792408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001520792408 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)c1ccccc1OCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 5, 5, 4, 5, 5, 5, 10, 27, 35, 35, 33, 35, 35, 4, 4, 4, 2, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 27, 27, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520792408 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520792408 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520792408/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520792408/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520792408 Building ZINC001520816116 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520816116' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520816116 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520816116 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520816116/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520816116 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/632 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1csc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)n1) `ZINC001520816116.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520816116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520816116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520816116 none CCCc1csc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 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: [10, 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, 10, 10, 10, 10, 10, 10, 10, 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: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520816116 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520816116/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520816116 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 633) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/633 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/633' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1csc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)n1) `ZINC001520816116.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520816116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520816116/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520816116 none CCCc1csc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 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: [10, 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, 10, 10, 10, 10, 10, 10, 10, 4, 2, 2, 2, 2, 10, 10, 3, 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: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520816116 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520816116 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520816116/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520816116/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520816116 Building ZINC001520816116 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520816116' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520816116 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520816116 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520816116/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520816116 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 632) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCCc1csc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)n1) `ZINC001520816116.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520816116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520816116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520816116 none CCCc1csc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 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: [10, 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, 10, 10, 10, 10, 10, 10, 10, 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: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520816116 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520816116/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520816116 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 633) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCCc1csc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)n1) `ZINC001520816116.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520816116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520816116/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001520816116 none CCCc1csc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 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: [10, 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, 10, 10, 10, 10, 10, 10, 10, 4, 2, 2, 2, 2, 10, 10, 3, 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: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520816116 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520816116 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520816116/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520816116/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520816116 Building ZINC001520872492 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520872492' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520872492 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520872492 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520872492/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520872492 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/634 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc2ccccc2n1C1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001520872492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520872492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520872492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001520872492 none CCc1nc2ccccc2n1C1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 16, 8, 2, 11, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 16, 16, 45, 45, 45, 45, 45, 32, 32, 32, 32, 16, 16, 16, 16, 16, 4, 1, 4, 16, 16, 16, 16] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 147 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520872492 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520872492/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520872492 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 635) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/635 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/635' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc2ccccc2n1C1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001520872492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520872492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520872492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001520872492 none CCc1nc2ccccc2n1C1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 36, 36, 36, 36, 36, 36, 36, 36, 18, 18, 18, 18, 7, 2, 9, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 18, 18, 45, 45, 45, 45, 45, 36, 36, 36, 36, 18, 18, 18, 18, 18, 3, 1, 3, 18, 18, 18, 18] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 123 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520872492 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520872492 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520872492/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520872492/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520872492 Building ZINC001520872492 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520872492' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520872492 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520872492 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520872492/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520872492 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 634) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCc1nc2ccccc2n1C1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001520872492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520872492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520872492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001520872492 none CCc1nc2ccccc2n1C1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 16, 8, 2, 11, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 16, 16, 45, 45, 45, 45, 45, 32, 32, 32, 32, 16, 16, 16, 16, 16, 4, 1, 4, 16, 16, 16, 16] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 147 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520872492 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520872492/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520872492 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 635) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCc1nc2ccccc2n1C1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001520872492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520872492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520872492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001520872492 none CCc1nc2ccccc2n1C1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 36, 36, 36, 36, 36, 36, 36, 36, 18, 18, 18, 18, 7, 2, 9, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 18, 18, 45, 45, 45, 45, 45, 36, 36, 36, 36, 18, 18, 18, 18, 18, 3, 1, 3, 18, 18, 18, 18] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 123 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520872492 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520872492 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520872492/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520872492/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520872492 Building ZINC001520909421 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520909421' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520909421 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520909421 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520909421/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520909421 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/636 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1scc(c2ccc(C)cc2)c1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001520909421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520909421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520909421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001520909421 none COC(=O)c1scc(c2ccc(C)cc2)c1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 14, 1, 1, 1, 1, 1, 1, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 12, 23, 12, 12, 12, 12, 12, 19, 19, 12, 16, 19, 19, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 12, 19, 19, 19, 19, 19, 19, 19, 4, 7, 7, 7, 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, 47, 48, 49, 50]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520909421 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520909421/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520909421 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 637) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/637 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/637' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1scc(c2ccc(C)cc2)c1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001520909421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520909421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520909421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001520909421 none COC(=O)c1scc(c2ccc(C)cc2)c1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 14, 1, 1, 1, 1, 1, 1, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 25, 15, 15, 15, 15, 15, 20, 20, 15, 15, 20, 20, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 25, 25, 25, 15, 20, 20, 20, 20, 20, 20, 20, 4, 7, 7, 7, 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, 47, 48, 49, 50]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520909421 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520909421 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520909421/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520909421/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520909421 Building ZINC001520909421 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520909421' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520909421 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520909421 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520909421/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520909421 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 636) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/636: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1scc(c2ccc(C)cc2)c1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001520909421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520909421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520909421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001520909421 none COC(=O)c1scc(c2ccc(C)cc2)c1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 14, 1, 1, 1, 1, 1, 1, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 12, 23, 12, 12, 12, 12, 12, 19, 19, 12, 16, 19, 19, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 12, 19, 19, 19, 19, 19, 19, 19, 4, 7, 7, 7, 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, 47, 48, 49, 50]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520909421 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520909421/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520909421 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 637) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/637: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1scc(c2ccc(C)cc2)c1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001520909421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520909421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520909421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001520909421 none COC(=O)c1scc(c2ccc(C)cc2)c1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 14, 1, 1, 1, 1, 1, 1, 5, 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, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 25, 15, 15, 15, 15, 15, 20, 20, 15, 15, 20, 20, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 25, 25, 25, 15, 20, 20, 20, 20, 20, 20, 20, 4, 7, 7, 7, 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, 47, 48, 49, 50]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520909421 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520909421 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520909421/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520909421/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520909421 Building ZINC001520923954 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520923954' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520923954 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520923954 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520923954/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520923954 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/638 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2ccc(C(F)(F)F)cc2Cl)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001520923954.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520923954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520923954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001520923954 none O=C(N1CCN(c2ccc(C(F)(F)F)cc2Cl)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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] 0 hydrogens 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, 10, 17, 17, 17, 17, 31, 31, 26, 31, 31, 31, 31, 31, 31, 31, 17, 17, 1, 1, 1, 4, 4, 4, 4, 4, 17, 17, 17, 17, 31, 31, 31, 17, 17, 17, 17, 4, 4] 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520923954 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520923954/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520923954 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 639) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/639 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/639' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2ccc(C(F)(F)F)cc2Cl)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001520923954.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520923954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520923954/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001520923954 none O=C(N1CCN(c2ccc(C(F)(F)F)cc2Cl)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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] 0 hydrogens 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, 10, 18, 18, 18, 18, 31, 31, 26, 31, 31, 31, 31, 31, 31, 31, 18, 18, 1, 1, 1, 4, 4, 4, 4, 4, 18, 18, 18, 18, 31, 31, 31, 18, 18, 18, 18, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520923954 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520923954 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520923954/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520923954/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520923954 Building ZINC001520923954 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520923954' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520923954 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520923954 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520923954/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520923954 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 638) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CCN(c2ccc(C(F)(F)F)cc2Cl)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001520923954.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520923954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520923954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001520923954 none O=C(N1CCN(c2ccc(C(F)(F)F)cc2Cl)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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] 0 hydrogens 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, 10, 17, 17, 17, 17, 31, 31, 26, 31, 31, 31, 31, 31, 31, 31, 17, 17, 1, 1, 1, 4, 4, 4, 4, 4, 17, 17, 17, 17, 31, 31, 31, 17, 17, 17, 17, 4, 4] 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520923954 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520923954/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520923954 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 639) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CCN(c2ccc(C(F)(F)F)cc2Cl)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001520923954.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520923954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520923954/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001520923954 none O=C(N1CCN(c2ccc(C(F)(F)F)cc2Cl)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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] 0 hydrogens 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, 10, 18, 18, 18, 18, 31, 31, 26, 31, 31, 31, 31, 31, 31, 31, 18, 18, 1, 1, 1, 4, 4, 4, 4, 4, 18, 18, 18, 18, 31, 31, 31, 18, 18, 18, 18, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520923954 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520923954 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520923954/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520923954/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520923954 Building ZINC001520949765 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520949765' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520949765 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520949765 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520949765/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520949765 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/640 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(Br)c1) `ZINC001520949765.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520949765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520949765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001520949765 none COc1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(Br)c1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 17, 1, 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, 7, 4, 9, 6, 8, 10, 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: [35, 8, 8, 22, 22, 8, 4, 8, 8, 4, 1, 4, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 22, 22, 22, 35, 35, 35, 22, 22, 8, 8, 8, 4, 5, 2, 5, 22] 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]) total number of confs: 133 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520949765 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520949765/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520949765 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 641) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/641 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/641' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(Br)c1) `ZINC001520949765.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520949765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520949765/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001520949765 none COc1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(Br)c1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 17, 1, 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, 7, 4, 9, 6, 8, 10, 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: [38, 11, 11, 25, 25, 11, 6, 11, 11, 6, 1, 6, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 25, 25, 25, 38, 38, 38, 25, 25, 11, 11, 11, 6, 5, 1, 5, 25] 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]) total number of confs: 141 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520949765 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520949765 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520949765/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520949765/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520949765 Building ZINC001520949765 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520949765' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520949765 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520949765 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520949765/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520949765 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 640) grep: /scratch/xiaobo/12845/xbi-8058088.35/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@H](C)NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(Br)c1) `ZINC001520949765.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520949765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520949765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001520949765 none COc1ccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(Br)c1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 17, 1, 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, 7, 4, 9, 6, 8, 10, 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: [35, 8, 8, 22, 22, 8, 4, 8, 8, 4, 1, 4, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 22, 22, 22, 35, 35, 35, 22, 22, 8, 8, 8, 4, 5, 2, 5, 22] 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]) total number of confs: 133 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520949765 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520949765/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520949765 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 641) grep: /scratch/xiaobo/12845/xbi-8058088.35/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@H](C)NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(Br)c1) `ZINC001520949765.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520949765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520949765/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001520949765 none COc1ccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(Br)c1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 17, 1, 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, 7, 4, 9, 6, 8, 10, 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: [38, 11, 11, 25, 25, 11, 6, 11, 11, 6, 1, 6, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 25, 25, 25, 38, 38, 38, 25, 25, 11, 11, 11, 6, 5, 1, 5, 25] 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]) total number of confs: 141 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520949765 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520949765 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520949765/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520949765/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520949765 Building ZINC001520978994 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978994' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978994 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520978994 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978994/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978994 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/642 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(c3ccc4c(c3)C[C@H](C)O4)cc2)cc1Cl) `ZINC001520978994.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520978994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001520978994 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(c3ccc4c(c3)C[C@H](C)O4)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', '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', '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, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 6, 7, 24, 28, 28, 28, 24, 28, 28, 28, 28, 28, 7, 7, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 7, 7, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 37] 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, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978994 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978994/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978994 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 643) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/643 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/643' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(c3ccc4c(c3)C[C@H](C)O4)cc2)cc1Cl) `ZINC001520978994.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520978994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978994/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001520978994 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(c3ccc4c(c3)C[C@H](C)O4)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', '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', '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, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 5, 7, 24, 27, 27, 27, 24, 27, 27, 27, 27, 27, 7, 7, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 7, 7, 27, 27, 27, 27, 27, 27, 27, 27, 7, 7, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 37] 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, 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/12845/xbi-8058088.35/working/building/ZINC001520978994 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520978994 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978994/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978994/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978994 Building ZINC001520978994 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978994' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978994 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520978994 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978994/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978994 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 642) grep: /scratch/xiaobo/12845/xbi-8058088.35/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)NCc2ccc(c3ccc4c(c3)C[C@H](C)O4)cc2)cc1Cl) `ZINC001520978994.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520978994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001520978994 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(c3ccc4c(c3)C[C@H](C)O4)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', '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', '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, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 6, 7, 24, 28, 28, 28, 24, 28, 28, 28, 28, 28, 7, 7, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 7, 7, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 37] 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, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978994 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978994/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978994 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 643) grep: /scratch/xiaobo/12845/xbi-8058088.35/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)NCc2ccc(c3ccc4c(c3)C[C@H](C)O4)cc2)cc1Cl) `ZINC001520978994.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520978994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978994/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001520978994 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(c3ccc4c(c3)C[C@H](C)O4)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', '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', '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, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 5, 7, 24, 27, 27, 27, 24, 27, 27, 27, 27, 27, 7, 7, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 7, 7, 27, 27, 27, 27, 27, 27, 27, 27, 7, 7, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 37] 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, 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/12845/xbi-8058088.35/working/building/ZINC001520978994 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520978994 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978994/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978994/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978994 Building ZINC001520978996 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978996' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978996 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520978996 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978996/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978996 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/644 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(c3ccc4c(c3)C[C@@H](C)O4)cc2)cc1Cl) `ZINC001520978996.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520978996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001520978996 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(c3ccc4c(c3)C[C@@H](C)O4)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', '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', '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, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 5, 7, 25, 28, 28, 28, 25, 28, 28, 28, 28, 28, 7, 7, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 7, 7, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 37] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978996 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978996/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978996 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 645) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/645 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/645' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(c3ccc4c(c3)C[C@@H](C)O4)cc2)cc1Cl) `ZINC001520978996.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520978996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001520978996 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(c3ccc4c(c3)C[C@@H](C)O4)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', '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', '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, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 5, 7, 25, 29, 29, 29, 25, 29, 29, 29, 29, 29, 7, 7, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 7, 7, 29, 29, 29, 29, 29, 29, 29, 29, 7, 7, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 37] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978996 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520978996 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978996/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978996/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978996 Building ZINC001520978996 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978996' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978996 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520978996 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978996/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978996 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 644) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(c3ccc4c(c3)C[C@@H](C)O4)cc2)cc1Cl) `ZINC001520978996.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520978996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001520978996 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccc(c3ccc4c(c3)C[C@@H](C)O4)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', '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', '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, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 5, 7, 25, 28, 28, 28, 25, 28, 28, 28, 28, 28, 7, 7, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 7, 7, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 37] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978996 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978996/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978996 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 645) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(c3ccc4c(c3)C[C@@H](C)O4)cc2)cc1Cl) `ZINC001520978996.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520978996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001520978996 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccc(c3ccc4c(c3)C[C@@H](C)O4)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', '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', '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, 1, 1, 1, 1, 5, 5, 7, 5, 12, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 5, 7, 25, 29, 29, 29, 25, 29, 29, 29, 29, 29, 7, 7, 2, 2, 2, 4, 4, 4, 2, 2, 1, 5, 5, 7, 7, 29, 29, 29, 29, 29, 29, 29, 29, 7, 7, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 37] 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978996 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520978996 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978996/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978996/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520978996 Building ZINC001520996054 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520996054' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520996054 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520996054 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520996054/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520996054 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/646 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(c2nc(c3ccccc3)no2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001520996054.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520996054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520996054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001520996054 none O=C(N1CCC(c2nc(c3ccccc3)no2)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', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', '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, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 9, 9, 9, 9, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 9, 9, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 9, 44, 44, 44, 44, 44, 9, 9, 9, 9, 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, 43, 44, 45]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520996054 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520996054/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520996054 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 647) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/647 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/647' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(c2nc(c3ccccc3)no2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001520996054.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520996054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520996054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001520996054 none O=C(N1CCC(c2nc(c3ccccc3)no2)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', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', '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, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 10, 10, 10, 10, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520996054 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520996054 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520996054/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520996054/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520996054 Building ZINC001520996054 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520996054' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520996054 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001520996054 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520996054/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520996054 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 646) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CCC(c2nc(c3ccccc3)no2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001520996054.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001520996054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520996054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001520996054 none O=C(N1CCC(c2nc(c3ccccc3)no2)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', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', '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, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 9, 9, 9, 9, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 9, 9, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 9, 9, 9, 44, 44, 44, 44, 44, 9, 9, 9, 9, 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, 43, 44, 45]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520996054 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520996054/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520996054 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 647) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CCC(c2nc(c3ccccc3)no2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001520996054.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001520996054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520996054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001520996054 none O=C(N1CCC(c2nc(c3ccccc3)no2)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', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', '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, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 12, 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] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 10, 10, 10, 10, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520996054 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001520996054 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520996054/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520996054/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001520996054 Building ZINC001521015564 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521015564' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521015564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521015564 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521015564/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521015564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/648 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/648' -> `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) `ZINC001521015564.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521015564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521015564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001521015564 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, 5, 8, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 23, 23, 23, 13, 23, 23, 23, 25, 37, 37, 8, 8, 8, 5, 8, 8, 23, 23, 23, 37] 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/12845/xbi-8058088.35/working/building/ZINC001521015564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521015564/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521015564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 649) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/649 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/649' -> `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) `ZINC001521015564.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521015564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521015564/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001521015564 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, 23, 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: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521015564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521015564 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521015564/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521015564/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521015564 Building ZINC001521015564 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521015564' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521015564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521015564 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521015564/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521015564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 648) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1cc(Cl)ccc1OC(F)F) `ZINC001521015564.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521015564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521015564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001521015564 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, 5, 8, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 23, 23, 23, 13, 23, 23, 23, 25, 37, 37, 8, 8, 8, 5, 8, 8, 23, 23, 23, 37] 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/12845/xbi-8058088.35/working/building/ZINC001521015564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521015564/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521015564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 649) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1cc(Cl)ccc1OC(F)F) `ZINC001521015564.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521015564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521015564/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001521015564 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, 23, 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: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521015564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521015564 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521015564/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521015564/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521015564 Building ZINC001521025359 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025359' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025359 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521025359 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025359/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025359 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/650 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/650' -> `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)Cc1c(Cl)cccc1Cl) `ZINC001521025359.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521025359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001521025359 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)Cc1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 16, 1, 1, 1, 1, 16, 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, 7, 7, 7] 0 hydrogens need 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, 5, 13, 13, 4, 4, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 29, 36, 36, 36, 34, 36, 36, 36, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 4, 5, 13, 13, 13, 29, 29, 36, 34, 36] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 174 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025359 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025359/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025359 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 651) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/651 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/651' -> `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)Cc1c(Cl)cccc1Cl) `ZINC001521025359.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521025359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001521025359 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)Cc1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 16, 1, 1, 1, 1, 16, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 30, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 3, 4, 13, 13, 13, 30, 30, 36, 36, 36] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 165 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025359 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521025359 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025359/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025359/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025359 Building ZINC001521025359 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025359' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025359 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521025359 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025359/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025359 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 650) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)Cc1c(Cl)cccc1Cl) `ZINC001521025359.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521025359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001521025359 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)Cc1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 16, 1, 1, 1, 1, 16, 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, 7, 7, 7] 0 hydrogens need 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, 5, 13, 13, 4, 4, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 29, 36, 36, 36, 34, 36, 36, 36, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 4, 5, 13, 13, 13, 29, 29, 36, 34, 36] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 174 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025359 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025359/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025359 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 651) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)Cc1c(Cl)cccc1Cl) `ZINC001521025359.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521025359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001521025359 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)Cc1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 16, 1, 1, 1, 1, 16, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 30, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 3, 4, 13, 13, 13, 30, 30, 36, 36, 36] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 165 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025359 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521025359 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025359/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025359/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025359 Building ZINC001521025361 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025361' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025361 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521025361 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025361/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025361 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/652 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)Cc1c(Cl)cccc1Cl) `ZINC001521025361.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521025361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001521025361 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)Cc1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 16, 1, 1, 1, 1, 16, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 13, 13, 13, 30, 35, 35, 35, 30, 35, 35, 35, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 4, 13, 13, 13, 30, 30, 35, 30, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 172 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025361 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025361/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025361 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 653) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/653 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/653' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)Cc1c(Cl)cccc1Cl) `ZINC001521025361.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521025361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025361/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001521025361 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)Cc1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 16, 1, 1, 1, 1, 16, 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, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 5, 13, 13, 13, 29, 36, 36, 36, 29, 36, 36, 36, 4, 4, 4, 13, 13, 6, 13, 13, 4, 4, 4, 5, 13, 13, 13, 29, 29, 36, 29, 36] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 195 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025361 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521025361 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025361/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025361/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025361 Building ZINC001521025361 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025361' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025361 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521025361 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025361/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025361 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 652) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/652: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)Cc1c(Cl)cccc1Cl) `ZINC001521025361.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521025361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001521025361 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)Cc1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 16, 1, 1, 1, 1, 16, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 13, 13, 13, 30, 35, 35, 35, 30, 35, 35, 35, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 4, 13, 13, 13, 30, 30, 35, 30, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 172 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025361 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025361/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025361 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 653) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/653: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)Cc1c(Cl)cccc1Cl) `ZINC001521025361.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521025361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025361/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001521025361 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)Cc1c(Cl)cccc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 16, 1, 1, 1, 1, 16, 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, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 5, 13, 13, 13, 29, 36, 36, 36, 29, 36, 36, 36, 4, 4, 4, 13, 13, 6, 13, 13, 4, 4, 4, 5, 13, 13, 13, 29, 29, 36, 29, 36] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 195 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025361 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521025361 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025361/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025361/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025361 Building ZINC001521025764 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025764' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025764 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521025764 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025764/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025764 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/654 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2c(C)c(C(C)(C)C)nn2c2ccccc2)cc1Cl) `ZINC001521025764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521025764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001521025764 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2c(C)c(C(C)(C)C)nn2c2ccccc2)cc1Cl NO_LONG_NAME dock atom 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.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 5, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 19, 19, 17, 19, 19, 6, 6, 6, 10, 10, 10, 6, 6, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 19, 19, 17, 19, 19, 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: 71 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025764 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025764/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025764 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 655) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/655 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/655' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2c(C)c(C(C)(C)C)nn2c2ccccc2)cc1Cl) `ZINC001521025764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521025764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001521025764 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2c(C)c(C(C)(C)C)nn2c2ccccc2)cc1Cl NO_LONG_NAME dock atom 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.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 5, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 2, 6, 6, 1, 1, 1, 1, 4, 4, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 19, 19, 16, 19, 19, 6, 6, 6, 10, 10, 10, 6, 6, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 19, 19, 16, 19, 19, 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: 72 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025764 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521025764 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025764/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025764/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025764 Building ZINC001521025764 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025764' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025764 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521025764 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025764/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025764 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 654) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2c(C)c(C(C)(C)C)nn2c2ccccc2)cc1Cl) `ZINC001521025764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521025764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001521025764 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2c(C)c(C(C)(C)C)nn2c2ccccc2)cc1Cl NO_LONG_NAME dock atom 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.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 5, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 19, 19, 17, 19, 19, 6, 6, 6, 10, 10, 10, 6, 6, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 19, 19, 17, 19, 19, 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: 71 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025764 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025764/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025764 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 655) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2c(C)c(C(C)(C)C)nn2c2ccccc2)cc1Cl) `ZINC001521025764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521025764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001521025764 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2c(C)c(C(C)(C)C)nn2c2ccccc2)cc1Cl NO_LONG_NAME dock atom 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.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 5, 1, 5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 2, 6, 6, 1, 1, 1, 1, 4, 4, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 19, 19, 16, 19, 19, 6, 6, 6, 10, 10, 10, 6, 6, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 19, 19, 16, 19, 19, 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: 72 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025764 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521025764 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025764/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025764/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521025764 Building ZINC001521071840 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071840' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071840 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521071840 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071840/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071840 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/656 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1c[nH]c2ccccc21)C(Cl)(Cl)Cl) `ZINC001521071840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521071840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001521071840 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1c[nH]c2ccccc21)C(Cl)(Cl)Cl 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', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'Cl', 'Cl', 'Cl', '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, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 2, 6, 6, 1, 1, 1, 1, 6, 6, 6, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 11, 27, 27, 27, 7, 7, 7, 6, 6, 6, 6, 6, 25, 25, 25, 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]) total number of confs: 160 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071840 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071840/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071840 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 657) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/657 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/657' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1c[nH]c2ccccc21)C(Cl)(Cl)Cl) `ZINC001521071840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521071840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001521071840 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1c[nH]c2ccccc21)C(Cl)(Cl)Cl 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', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'Cl', 'Cl', 'Cl', '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, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 3, 5, 5, 1, 1, 1, 1, 7, 7, 7, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29, 13, 26, 26, 26, 6, 6, 6, 5, 5, 5, 5, 7, 29, 29, 29, 29, 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]) total number of confs: 156 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071840 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521071840 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071840/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071840/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071840 Building ZINC001521071840 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071840' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071840 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521071840 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071840/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071840 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 656) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1c[nH]c2ccccc21)C(Cl)(Cl)Cl) `ZINC001521071840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521071840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001521071840 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1c[nH]c2ccccc21)C(Cl)(Cl)Cl 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', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'Cl', 'Cl', 'Cl', '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, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 2, 6, 6, 1, 1, 1, 1, 6, 6, 6, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 11, 27, 27, 27, 7, 7, 7, 6, 6, 6, 6, 6, 25, 25, 25, 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]) total number of confs: 160 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071840 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071840/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071840 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 657) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1c[nH]c2ccccc21)C(Cl)(Cl)Cl) `ZINC001521071840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521071840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001521071840 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](c1c[nH]c2ccccc21)C(Cl)(Cl)Cl 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', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'Cl', 'Cl', 'Cl', '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, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 3, 5, 5, 1, 1, 1, 1, 7, 7, 7, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29, 13, 26, 26, 26, 6, 6, 6, 5, 5, 5, 5, 7, 29, 29, 29, 29, 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]) total number of confs: 156 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071840 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521071840 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071840/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071840/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071840 Building ZINC001521071841 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071841' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071841 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521071841 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071841/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071841 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/658 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1c[nH]c2ccccc21)C(Cl)(Cl)Cl) `ZINC001521071841.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521071841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001521071841 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1c[nH]c2ccccc21)C(Cl)(Cl)Cl 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', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'Cl', 'Cl', 'Cl', '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, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 3, 5, 5, 1, 1, 1, 1, 7, 7, 7, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29, 13, 27, 27, 27, 6, 6, 6, 5, 5, 5, 5, 7, 29, 29, 29, 29, 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]) total number of confs: 159 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071841 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071841/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071841 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 659) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/659 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/659' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](c1c[nH]c2ccccc21)C(Cl)(Cl)Cl) `ZINC001521071841.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521071841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071841/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001521071841 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](c1c[nH]c2ccccc21)C(Cl)(Cl)Cl 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', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'Cl', 'Cl', 'Cl', '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, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 2, 6, 6, 1, 1, 1, 1, 6, 6, 6, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 11, 27, 27, 27, 7, 7, 7, 6, 6, 6, 6, 6, 25, 25, 25, 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]) total number of confs: 163 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071841 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521071841 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071841/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071841/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071841 Building ZINC001521071841 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071841' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071841 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521071841 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071841/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071841 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 658) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1c[nH]c2ccccc21)C(Cl)(Cl)Cl) `ZINC001521071841.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521071841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001521071841 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](c1c[nH]c2ccccc21)C(Cl)(Cl)Cl 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', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'Cl', 'Cl', 'Cl', '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, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 3, 5, 5, 1, 1, 1, 1, 7, 7, 7, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29, 13, 27, 27, 27, 6, 6, 6, 5, 5, 5, 5, 7, 29, 29, 29, 29, 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]) total number of confs: 159 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071841 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071841/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071841 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 659) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](c1c[nH]c2ccccc21)C(Cl)(Cl)Cl) `ZINC001521071841.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521071841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071841/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001521071841 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](c1c[nH]c2ccccc21)C(Cl)(Cl)Cl 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', 'H', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'Cl', 'Cl', 'Cl', '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, 7, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 2, 6, 6, 1, 1, 1, 1, 6, 6, 6, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 11, 27, 27, 27, 7, 7, 7, 6, 6, 6, 6, 6, 25, 25, 25, 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]) total number of confs: 163 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071841 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521071841 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071841/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071841/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521071841 Building ZINC001521093176 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521093176' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521093176 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521093176 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521093176/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521093176 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/660 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Cc1cccs1)Nc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001521093176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521093176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521093176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521093176 none O=C(Cc1cccs1)Nc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 14, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens 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, 37, 48, 48, 48, 48, 10, 10, 10, 8, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 37, 37, 48, 48, 48, 11, 10, 10, 10, 10, 3, 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]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521093176 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521093176/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521093176 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 661) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/661 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/661' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Cc1cccs1)Nc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001521093176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521093176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521093176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521093176 none O=C(Cc1cccs1)Nc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 14, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens 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, 38, 48, 48, 48, 48, 10, 10, 10, 8, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 38, 38, 48, 48, 48, 11, 10, 10, 10, 10, 3, 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521093176 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521093176 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521093176/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521093176/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521093176 Building ZINC001521093176 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521093176' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521093176 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521093176 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521093176/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521093176 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 660) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(Cc1cccs1)Nc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001521093176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521093176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521093176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521093176 none O=C(Cc1cccs1)Nc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 14, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens 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, 37, 48, 48, 48, 48, 10, 10, 10, 8, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 37, 37, 48, 48, 48, 11, 10, 10, 10, 10, 3, 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]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521093176 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521093176/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521093176 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 661) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(Cc1cccs1)Nc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001521093176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521093176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521093176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521093176 none O=C(Cc1cccs1)Nc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 14, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens 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, 38, 48, 48, 48, 48, 10, 10, 10, 8, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 38, 38, 48, 48, 48, 11, 10, 10, 10, 10, 3, 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521093176 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521093176 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521093176/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521093176/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521093176 Building ZINC001521129894 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521129894' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521129894 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521129894 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521129894/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521129894 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/662 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2nc(N(Cc3ccccc3)C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)sc2c1) `ZINC001521129894.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521129894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521129894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521129894 none COc1ccc2nc(N(Cc3ccccc3)C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)sc2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 14, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 13, 12, 6, 12, 23, 23, 23, 23, 23, 23, 1, 6, 1, 1, 1, 6, 6, 3, 6, 6, 6, 6, 13, 13, 13, 18, 18, 18, 13, 13, 23, 23, 23, 23, 23, 23, 23, 6, 6, 6, 6, 6, 6, 6, 13] 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]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521129894 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521129894/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521129894 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 663) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/663 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/663' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2nc(N(Cc3ccccc3)C(=O)[C@]([O-])([SiH3])c3ccccc3OC)sc2c1) `ZINC001521129894.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521129894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521129894/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521129894 none COc1ccc2nc(N(Cc3ccccc3)C(=O)[C@]([O-])([SiH3])c3ccccc3OC)sc2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 14, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 14, 14, 12, 6, 12, 24, 24, 24, 24, 24, 24, 1, 6, 1, 1, 1, 6, 6, 3, 6, 6, 6, 7, 14, 14, 14, 19, 19, 19, 14, 14, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 7, 7, 7, 14] 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521129894 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521129894 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521129894/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521129894/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521129894 Building ZINC001521129894 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521129894' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521129894 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521129894 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521129894/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521129894 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 662) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc2nc(N(Cc3ccccc3)C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)sc2c1) `ZINC001521129894.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521129894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521129894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521129894 none COc1ccc2nc(N(Cc3ccccc3)C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)sc2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 14, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 13, 12, 6, 12, 23, 23, 23, 23, 23, 23, 1, 6, 1, 1, 1, 6, 6, 3, 6, 6, 6, 6, 13, 13, 13, 18, 18, 18, 13, 13, 23, 23, 23, 23, 23, 23, 23, 6, 6, 6, 6, 6, 6, 6, 13] 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]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521129894 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521129894/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521129894 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 663) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc2nc(N(Cc3ccccc3)C(=O)[C@]([O-])([SiH3])c3ccccc3OC)sc2c1) `ZINC001521129894.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521129894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521129894/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521129894 none COc1ccc2nc(N(Cc3ccccc3)C(=O)[C@]([O-])([SiH3])c3ccccc3OC)sc2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 14, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 14, 14, 12, 6, 12, 24, 24, 24, 24, 24, 24, 1, 6, 1, 1, 1, 6, 6, 3, 6, 6, 6, 7, 14, 14, 14, 19, 19, 19, 14, 14, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 7, 7, 7, 14] 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521129894 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521129894 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521129894/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521129894/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521129894 Building ZINC001521141582 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141582' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141582 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521141582 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141582/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141582 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/664 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](COc2ccccc2Cl)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001521141582.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521141582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521141582 none O=C(N1CCC[C@@H](COc2ccccc2Cl)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.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 3, 3, 3, 3, 3, 3, 9, 26, 36, 36, 26, 36, 36, 36, 3, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 9, 9, 36, 36, 35, 36, 3, 3, 2, 2] 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141582 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141582/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141582 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 665) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/665 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/665' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](COc2ccccc2Cl)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001521141582.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521141582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141582/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521141582 none O=C(N1CCC[C@@H](COc2ccccc2Cl)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.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 3, 3, 3, 3, 3, 3, 11, 27, 38, 38, 27, 38, 38, 38, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 38, 38, 38, 38, 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141582 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521141582 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141582/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141582/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141582 Building ZINC001521141582 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141582' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141582 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521141582 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141582/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141582 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 664) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CCC[C@@H](COc2ccccc2Cl)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001521141582.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521141582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521141582 none O=C(N1CCC[C@@H](COc2ccccc2Cl)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.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 3, 3, 3, 3, 3, 3, 9, 26, 36, 36, 26, 36, 36, 36, 3, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 9, 9, 36, 36, 35, 36, 3, 3, 2, 2] 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141582 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141582/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141582 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 665) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CCC[C@@H](COc2ccccc2Cl)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001521141582.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521141582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141582/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521141582 none O=C(N1CCC[C@@H](COc2ccccc2Cl)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.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 3, 3, 3, 3, 3, 3, 11, 27, 38, 38, 27, 38, 38, 38, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 38, 38, 38, 38, 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]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141582 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521141582 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141582/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141582/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141582 Building ZINC001521141584 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141584' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141584 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521141584 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141584/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141584 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/666 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](COc2ccccc2Cl)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001521141584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521141584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521141584 none O=C(N1CCC[C@H](COc2ccccc2Cl)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.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 3, 3, 3, 3, 3, 3, 11, 26, 36, 36, 26, 36, 36, 36, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 36, 36, 36, 36, 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]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141584 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141584/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141584 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 667) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/667 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/667' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](COc2ccccc2Cl)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001521141584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521141584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521141584 none O=C(N1CCC[C@H](COc2ccccc2Cl)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.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 3, 3, 3, 3, 3, 3, 10, 27, 37, 37, 27, 37, 37, 37, 3, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 10, 10, 37, 37, 35, 37, 3, 3, 2, 2] 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: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141584 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521141584 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141584/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141584/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141584 Building ZINC001521141584 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141584' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141584 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521141584 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141584/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141584 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 666) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CCC[C@H](COc2ccccc2Cl)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001521141584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521141584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521141584 none O=C(N1CCC[C@H](COc2ccccc2Cl)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.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 3, 3, 3, 3, 3, 3, 11, 26, 36, 36, 26, 36, 36, 36, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 36, 36, 36, 36, 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]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141584 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141584/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141584 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 667) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CCC[C@H](COc2ccccc2Cl)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001521141584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521141584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521141584 none O=C(N1CCC[C@H](COc2ccccc2Cl)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.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 16, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 3, 3, 3, 3, 3, 3, 10, 27, 37, 37, 27, 37, 37, 37, 3, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 10, 10, 37, 37, 35, 37, 3, 3, 2, 2] 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: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141584 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521141584 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141584/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141584/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521141584 Building ZINC001521157533 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521157533' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521157533 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521157533 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521157533/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521157533 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/668 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)OC(C)(C)C)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001521157533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521157533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521157533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521157533 none Cc1ccc(NC(=O)OC(C)(C)C)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 5, 27, 36, 36, 39, 39, 39, 39, 5, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 27, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 2, 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521157533 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521157533/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521157533 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 669) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/669 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/669' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)OC(C)(C)C)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001521157533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521157533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521157533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521157533 none Cc1ccc(NC(=O)OC(C)(C)C)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 5, 27, 36, 36, 40, 40, 40, 40, 5, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 27, 40, 40, 40, 40, 40, 40, 40, 40, 40, 5, 2, 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521157533 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521157533 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521157533/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521157533/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521157533 Building ZINC001521157533 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521157533' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521157533 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521157533 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521157533/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521157533 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 668) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc(NC(=O)OC(C)(C)C)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001521157533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521157533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521157533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521157533 none Cc1ccc(NC(=O)OC(C)(C)C)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 5, 27, 36, 36, 39, 39, 39, 39, 5, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 27, 39, 39, 39, 39, 39, 39, 39, 39, 39, 5, 2, 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521157533 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521157533/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521157533 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 669) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc(NC(=O)OC(C)(C)C)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001521157533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521157533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521157533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521157533 none Cc1ccc(NC(=O)OC(C)(C)C)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', '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', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 5, 27, 36, 36, 40, 40, 40, 40, 5, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 27, 40, 40, 40, 40, 40, 40, 40, 40, 40, 5, 2, 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521157533 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521157533 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521157533/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521157533/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521157533 Building ZINC001521195557 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521195557' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521195557 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521195557 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521195557/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521195557 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/670 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)c2c(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)sc3c2CCCC3)cc1) `ZINC001521195557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521195557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521195557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001521195557 none COc1ccc(C(=O)c2c(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)sc3c2CCCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', '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', 'S.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 14, 1, 1, 5, 5, 5, 5, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 47, 47, 48, 48, 43, 27, 43, 27, 6, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 27, 27, 27, 27, 27, 27, 27, 48, 48, 48, 48, 48, 48, 48, 6, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 48, 48] 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521195557 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521195557/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521195557 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 671) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/671 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/671' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)c2c(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)sc3c2CCCC3)cc1) `ZINC001521195557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521195557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521195557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001521195557 none COc1ccc(C(=O)c2c(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)sc3c2CCCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', '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', 'S.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 14, 1, 1, 5, 5, 5, 5, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 42, 28, 42, 28, 6, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 28, 28, 28, 28, 28, 28, 28, 48, 48, 48, 48, 48, 48, 48, 6, 5, 5, 5, 5, 28, 28, 28, 28, 28, 28, 28, 28, 48, 48] 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521195557 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521195557 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521195557/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521195557/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521195557 Building ZINC001521195557 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521195557' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521195557 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521195557 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521195557/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521195557 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 670) grep: /scratch/xiaobo/12845/xbi-8058088.35/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)c2c(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)sc3c2CCCC3)cc1) `ZINC001521195557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521195557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521195557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001521195557 none COc1ccc(C(=O)c2c(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)sc3c2CCCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', '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', 'S.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 14, 1, 1, 5, 5, 5, 5, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 47, 47, 48, 48, 43, 27, 43, 27, 6, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 27, 27, 27, 27, 27, 27, 27, 48, 48, 48, 48, 48, 48, 48, 6, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 48, 48] 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521195557 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521195557/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521195557 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 671) grep: /scratch/xiaobo/12845/xbi-8058088.35/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)c2c(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)sc3c2CCCC3)cc1) `ZINC001521195557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521195557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521195557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001521195557 none COc1ccc(C(=O)c2c(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)sc3c2CCCC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', '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', 'S.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 14, 1, 1, 5, 5, 5, 5, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 42, 28, 42, 28, 6, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 28, 28, 28, 28, 28, 28, 28, 48, 48, 48, 48, 48, 48, 48, 6, 5, 5, 5, 5, 28, 28, 28, 28, 28, 28, 28, 28, 48, 48] 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521195557 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521195557 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521195557/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521195557/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521195557 Building ZINC001521308454 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521308454' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521308454 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521308454 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521308454/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521308454 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/672 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)c2ccc(C)cc2)CCCCC3)cn1) `ZINC001521308454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521308454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521308454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521308454 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)c2ccc(C)cc2)CCCCC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 13, 22, 22, 13, 22, 24, 24, 24, 24, 24, 24, 24, 24, 22, 22, 22, 22, 22, 6, 6, 12, 12, 12, 12, 12, 6, 3, 24, 24, 24, 24, 24, 24, 24, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 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: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521308454 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521308454/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521308454 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 673) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/673 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/673' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)c2ccc(C)cc2)CCCCC3)cn1) `ZINC001521308454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521308454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521308454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521308454 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)c2ccc(C)cc2)CCCCC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 13, 22, 22, 13, 22, 24, 24, 24, 24, 24, 24, 24, 24, 22, 22, 22, 22, 22, 6, 6, 15, 15, 15, 15, 15, 6, 3, 24, 24, 24, 24, 24, 24, 24, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 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: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521308454 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521308454 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521308454/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521308454/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521308454 Building ZINC001521308454 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521308454' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521308454 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521308454 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521308454/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521308454 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 672) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)c2ccc(C)cc2)CCCCC3)cn1) `ZINC001521308454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521308454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521308454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521308454 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)c2ccc(C)cc2)CCCCC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 13, 22, 22, 13, 22, 24, 24, 24, 24, 24, 24, 24, 24, 22, 22, 22, 22, 22, 6, 6, 12, 12, 12, 12, 12, 6, 3, 24, 24, 24, 24, 24, 24, 24, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 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: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521308454 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521308454/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521308454 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 673) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)c2ccc(C)cc2)CCCCC3)cn1) `ZINC001521308454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521308454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521308454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521308454 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2sc3c(c2C(=O)c2ccc(C)cc2)CCCCC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 13, 22, 22, 13, 22, 24, 24, 24, 24, 24, 24, 24, 24, 22, 22, 22, 22, 22, 6, 6, 15, 15, 15, 15, 15, 6, 3, 24, 24, 24, 24, 24, 24, 24, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 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: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521308454 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521308454 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521308454/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521308454/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521308454 Building ZINC001521385276 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521385276' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521385276 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521385276 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521385276/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521385276 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/674 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1COc1cccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1C) `ZINC001521385276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521385276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521385276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001521385276 none COc1ccccc1COc1cccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1C 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.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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 49, 43, 49, 49, 26, 16, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 50, 50, 50, 49, 49, 49, 49, 26, 26, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521385276 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521385276/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521385276 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 675) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/675 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/675' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1COc1cccc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1C) `ZINC001521385276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521385276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521385276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001521385276 none COc1ccccc1COc1cccc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1C 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.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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 48, 48, 25, 15, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 48, 48, 48, 48, 48, 48, 48, 25, 25, 6, 6, 6, 2, 3, 3, 3, 3, 3, 3, 3, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521385276 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521385276 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521385276/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521385276/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521385276 Building ZINC001521385276 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521385276' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521385276 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521385276 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521385276/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521385276 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 674) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccccc1COc1cccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1C) `ZINC001521385276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521385276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521385276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001521385276 none COc1ccccc1COc1cccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1C 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.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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 49, 43, 49, 49, 26, 16, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 50, 50, 50, 49, 49, 49, 49, 26, 26, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521385276 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521385276/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521385276 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 675) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccccc1COc1cccc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1C) `ZINC001521385276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521385276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521385276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001521385276 none COc1ccccc1COc1cccc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1C 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.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', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 48, 48, 25, 15, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 48, 48, 48, 48, 48, 48, 48, 25, 25, 6, 6, 6, 2, 3, 3, 3, 3, 3, 3, 3, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521385276 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521385276 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521385276/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521385276/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521385276 Building ZINC001521392485 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521392485' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521392485 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521392485 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521392485/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521392485 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/676 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/676' -> `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)NC1(c2ccc(F)cc2F)CCCCC1) `ZINC001521392485.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521392485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521392485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001521392485 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1(c2ccc(F)cc2F)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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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, 5, 1, 1, 1, 1, 15, 1, 1, 15, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 3, 5, 5, 2, 2, 1, 1, 1, 1, 6, 6, 11, 21, 35, 35, 30, 35, 35, 35, 35, 21, 21, 21, 21, 21, 2, 2, 2, 5, 5, 3, 5, 5, 2, 2, 2, 6, 35, 35, 35, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 119 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521392485 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521392485/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521392485 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 677) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/677 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/677' -> `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)NC1(c2ccc(F)cc2F)CCCCC1) `ZINC001521392485.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521392485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521392485/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001521392485 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1(c2ccc(F)cc2F)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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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, 5, 1, 1, 1, 1, 15, 1, 1, 15, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 6, 6, 11, 20, 36, 36, 31, 36, 36, 36, 36, 20, 20, 20, 20, 20, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 6, 36, 36, 36, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 118 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521392485 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521392485 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521392485/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521392485/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521392485 Building ZINC001521392485 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521392485' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521392485 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521392485 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521392485/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521392485 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 676) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1(c2ccc(F)cc2F)CCCCC1) `ZINC001521392485.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521392485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521392485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001521392485 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1(c2ccc(F)cc2F)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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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, 5, 1, 1, 1, 1, 15, 1, 1, 15, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 3, 5, 5, 2, 2, 1, 1, 1, 1, 6, 6, 11, 21, 35, 35, 30, 35, 35, 35, 35, 21, 21, 21, 21, 21, 2, 2, 2, 5, 5, 3, 5, 5, 2, 2, 2, 6, 35, 35, 35, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 119 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521392485 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521392485/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521392485 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 677) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1(c2ccc(F)cc2F)CCCCC1) `ZINC001521392485.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521392485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521392485/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001521392485 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1(c2ccc(F)cc2F)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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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, 5, 1, 1, 1, 1, 15, 1, 1, 15, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 1, 1, 1, 1, 6, 6, 11, 20, 36, 36, 31, 36, 36, 36, 36, 20, 20, 20, 20, 20, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 6, 36, 36, 36, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 118 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521392485 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521392485 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521392485/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521392485/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521392485 Building ZINC001521411664 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521411664' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521411664 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521411664 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521411664/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521411664 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/678 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Br)c(C(F)(F)F)c2)cc1Cl) `ZINC001521411664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521411664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521411664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001521411664 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Br)c(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', 'C.ar', 'Br', '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, 1, 17, 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: [13, 6, 5, 6, 6, 1, 1, 1, 1, 2, 2, 2, 14, 14, 8, 8, 14, 14, 14, 14, 14, 14, 6, 6, 6, 13, 13, 13, 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: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521411664 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521411664/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521411664 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 679) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/679 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/679' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Br)c(C(F)(F)F)c2)cc1Cl) `ZINC001521411664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521411664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521411664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001521411664 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Br)c(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', 'C.ar', 'Br', '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, 1, 17, 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, 3, 14, 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: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521411664 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521411664 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521411664/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521411664/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521411664 Building ZINC001521411664 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521411664' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521411664 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521411664 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521411664/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521411664 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 678) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Br)c(C(F)(F)F)c2)cc1Cl) `ZINC001521411664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521411664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521411664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001521411664 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Br)c(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', 'C.ar', 'Br', '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, 1, 17, 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: [13, 6, 5, 6, 6, 1, 1, 1, 1, 2, 2, 2, 14, 14, 8, 8, 14, 14, 14, 14, 14, 14, 6, 6, 6, 13, 13, 13, 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: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521411664 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521411664/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521411664 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 679) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Br)c(C(F)(F)F)c2)cc1Cl) `ZINC001521411664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521411664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521411664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001521411664 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Br)c(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', 'C.ar', 'Br', '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, 1, 17, 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, 3, 14, 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: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521411664 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521411664 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521411664/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521411664/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521411664 Building ZINC001521419808 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419808' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419808 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521419808 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419808/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419808 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/680 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCc3sc(c4ccc(F)cc4)nc32)cc1Cl) `ZINC001521419808.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521419808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001521419808 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCc3sc(c4ccc(F)cc4)nc32)cc1Cl NO_LONG_NAME dock atom 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', 'C.3', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 14, 1, 1, 1, 1, 1, 15, 1, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 7, 7, 1, 1, 1, 1, 5, 5, 9, 14, 14, 14, 14, 14, 14, 14, 14, 20, 20, 20, 20, 20, 20, 14, 14, 7, 7, 7, 14, 14, 14, 7, 7, 5, 14, 14, 14, 14, 14, 14, 20, 20, 20, 20, 7] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 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: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419808 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419808/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419808 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 681) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/681 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/681' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCc3sc(c4ccc(F)cc4)nc32)cc1Cl) `ZINC001521419808.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521419808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001521419808 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCc3sc(c4ccc(F)cc4)nc32)cc1Cl NO_LONG_NAME dock atom 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', 'C.3', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 14, 1, 1, 1, 1, 1, 15, 1, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 9, 14, 14, 14, 14, 14, 14, 14, 14, 17, 17, 17, 17, 17, 17, 14, 14, 6, 6, 6, 12, 12, 12, 6, 6, 5, 14, 14, 14, 14, 14, 14, 17, 17, 17, 17, 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419808 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521419808 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419808/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419808/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419808 Building ZINC001521419808 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419808' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419808 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521419808 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419808/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419808 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 680) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCc3sc(c4ccc(F)cc4)nc32)cc1Cl) `ZINC001521419808.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521419808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001521419808 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCc3sc(c4ccc(F)cc4)nc32)cc1Cl NO_LONG_NAME dock atom 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', 'C.3', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 14, 1, 1, 1, 1, 1, 15, 1, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 7, 7, 1, 1, 1, 1, 5, 5, 9, 14, 14, 14, 14, 14, 14, 14, 14, 20, 20, 20, 20, 20, 20, 14, 14, 7, 7, 7, 14, 14, 14, 7, 7, 5, 14, 14, 14, 14, 14, 14, 20, 20, 20, 20, 7] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 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: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419808 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419808/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419808 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 681) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCc3sc(c4ccc(F)cc4)nc32)cc1Cl) `ZINC001521419808.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521419808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001521419808 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCc3sc(c4ccc(F)cc4)nc32)cc1Cl NO_LONG_NAME dock atom 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', 'C.3', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 14, 1, 1, 1, 1, 1, 15, 1, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 9, 14, 14, 14, 14, 14, 14, 14, 14, 17, 17, 17, 17, 17, 17, 14, 14, 6, 6, 6, 12, 12, 12, 6, 6, 5, 14, 14, 14, 14, 14, 14, 17, 17, 17, 17, 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419808 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521419808 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419808/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419808/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419808 Building ZINC001521419809 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419809' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419809 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521419809 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419809/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419809 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/682 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCc3sc(c4ccc(F)cc4)nc32)cc1Cl) `ZINC001521419809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521419809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001521419809 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCc3sc(c4ccc(F)cc4)nc32)cc1Cl NO_LONG_NAME dock atom 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', 'C.3', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 14, 1, 1, 1, 1, 1, 15, 1, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 1, 1, 1, 5, 5, 7, 13, 13, 13, 13, 13, 13, 13, 13, 23, 23, 23, 23, 23, 23, 13, 13, 6, 6, 6, 12, 12, 12, 6, 6, 5, 13, 13, 13, 13, 13, 13, 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, 43, 44, 45, 46, 47]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419809 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419809/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419809 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 683) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/683 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/683' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCc3sc(c4ccc(F)cc4)nc32)cc1Cl) `ZINC001521419809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521419809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001521419809 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCc3sc(c4ccc(F)cc4)nc32)cc1Cl NO_LONG_NAME dock atom 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', 'C.3', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 14, 1, 1, 1, 1, 1, 15, 1, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 21, 21, 21, 21, 11, 11, 6, 6, 6, 12, 12, 12, 6, 6, 4, 11, 11, 11, 11, 11, 11, 21, 21, 21, 21, 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419809 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521419809 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419809/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419809/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419809 Building ZINC001521419809 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419809' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419809 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521419809 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419809/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419809 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 682) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCc3sc(c4ccc(F)cc4)nc32)cc1Cl) `ZINC001521419809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521419809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001521419809 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCc3sc(c4ccc(F)cc4)nc32)cc1Cl NO_LONG_NAME dock atom 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', 'C.3', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 14, 1, 1, 1, 1, 1, 15, 1, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 1, 1, 1, 5, 5, 7, 13, 13, 13, 13, 13, 13, 13, 13, 23, 23, 23, 23, 23, 23, 13, 13, 6, 6, 6, 12, 12, 12, 6, 6, 5, 13, 13, 13, 13, 13, 13, 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, 43, 44, 45, 46, 47]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419809 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419809/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419809 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 683) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCc3sc(c4ccc(F)cc4)nc32)cc1Cl) `ZINC001521419809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521419809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001521419809 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCc3sc(c4ccc(F)cc4)nc32)cc1Cl NO_LONG_NAME dock atom 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', 'C.3', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 1, 14, 1, 1, 1, 1, 1, 15, 1, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 21, 21, 21, 21, 11, 11, 6, 6, 6, 12, 12, 12, 6, 6, 4, 11, 11, 11, 11, 11, 11, 21, 21, 21, 21, 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419809 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521419809 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419809/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419809/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521419809 Building ZINC001521453508 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521453508' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521453508 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521453508 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521453508/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521453508 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/684 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(c2ccc3c(c2)OCCO3)cs1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001521453508.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521453508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521453508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521453508 none O=C(Nc1nc(c2ccc3c(c2)OCCO3)cs1)[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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 14, 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, 7, 7, 3, 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] 0 hydrogens need 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, 37, 37, 37, 37, 37, 37, 37, 37, 37, 5, 5, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 37, 37, 37, 37, 37, 37, 37, 5, 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521453508 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521453508/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521453508 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 685) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/685 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/685' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(c2ccc3c(c2)OCCO3)cs1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001521453508.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521453508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521453508/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521453508 none O=C(Nc1nc(c2ccc3c(c2)OCCO3)cs1)[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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 14, 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, 7, 7, 3, 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] 0 hydrogens need rotated 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, 36, 36, 36, 36, 36, 36, 36, 36, 36, 4, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 36, 36, 36, 36, 36, 36, 36, 4, 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521453508 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521453508 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521453508/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521453508/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521453508 Building ZINC001521453508 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521453508' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521453508 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521453508 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521453508/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521453508 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 684) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(Nc1nc(c2ccc3c(c2)OCCO3)cs1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001521453508.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521453508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521453508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521453508 none O=C(Nc1nc(c2ccc3c(c2)OCCO3)cs1)[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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 14, 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, 7, 7, 3, 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] 0 hydrogens need 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, 37, 37, 37, 37, 37, 37, 37, 37, 37, 5, 5, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 37, 37, 37, 37, 37, 37, 37, 5, 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521453508 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521453508/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521453508 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 685) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(Nc1nc(c2ccc3c(c2)OCCO3)cs1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001521453508.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521453508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521453508/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521453508 none O=C(Nc1nc(c2ccc3c(c2)OCCO3)cs1)[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.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 1, 14, 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, 7, 7, 3, 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] 0 hydrogens need rotated 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, 36, 36, 36, 36, 36, 36, 36, 36, 36, 4, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 36, 36, 36, 36, 36, 36, 36, 4, 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521453508 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521453508 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521453508/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521453508/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521453508 Building ZINC001521573594 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573594' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573594 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521573594 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573594/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573594 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/686 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](Cc2ccccc2)c2nc3ccccc3s2)cn1) `ZINC001521573594.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521573594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521573594 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](Cc2ccccc2)c2nc3ccccc3s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 14, 14, 7, 7, 1, 1, 1, 1, 4, 4, 4, 6, 6, 13, 13, 13, 13, 13, 13, 6, 20, 20, 20, 20, 20, 20, 20, 20, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 4, 13, 13, 13, 13, 13, 13, 13, 20, 20, 20, 20, 7] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573594 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573594/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573594 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 687) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/687 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/687' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H](Cc2ccccc2)c2nc3ccccc3s2)cn1) `ZINC001521573594.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521573594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573594/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521573594 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H](Cc2ccccc2)c2nc3ccccc3s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 7, 15, 15, 7, 7, 1, 1, 1, 1, 4, 4, 4, 6, 6, 14, 14, 14, 14, 14, 14, 6, 20, 20, 20, 20, 20, 20, 20, 20, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 4, 14, 14, 14, 14, 14, 14, 14, 20, 20, 20, 20, 7] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573594 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521573594 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573594/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573594/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573594 Building ZINC001521573594 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573594' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573594 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521573594 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573594/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573594 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 686) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/686: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](Cc2ccccc2)c2nc3ccccc3s2)cn1) `ZINC001521573594.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521573594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521573594 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](Cc2ccccc2)c2nc3ccccc3s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 14, 14, 7, 7, 1, 1, 1, 1, 4, 4, 4, 6, 6, 13, 13, 13, 13, 13, 13, 6, 20, 20, 20, 20, 20, 20, 20, 20, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 4, 13, 13, 13, 13, 13, 13, 13, 20, 20, 20, 20, 7] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573594 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573594/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573594 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 687) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/687: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H](Cc2ccccc2)c2nc3ccccc3s2)cn1) `ZINC001521573594.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521573594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573594/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521573594 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H](Cc2ccccc2)c2nc3ccccc3s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 7, 15, 15, 7, 7, 1, 1, 1, 1, 4, 4, 4, 6, 6, 14, 14, 14, 14, 14, 14, 6, 20, 20, 20, 20, 20, 20, 20, 20, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 4, 14, 14, 14, 14, 14, 14, 14, 20, 20, 20, 20, 7] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573594 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521573594 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573594/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573594/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573594 Building ZINC001521573595 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573595' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573595 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521573595 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573595/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573595 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/688 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H](Cc2ccccc2)c2nc3ccccc3s2)cn1) `ZINC001521573595.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521573595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521573595 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H](Cc2ccccc2)c2nc3ccccc3s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 13, 13, 13, 13, 13, 13, 6, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 4, 13, 13, 13, 13, 13, 13, 13, 19, 19, 19, 19, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573595 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573595/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573595 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 689) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/689 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/689' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H](Cc2ccccc2)c2nc3ccccc3s2)cn1) `ZINC001521573595.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521573595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573595/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521573595 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H](Cc2ccccc2)c2nc3ccccc3s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 14, 14, 7, 7, 1, 1, 1, 1, 4, 4, 4, 6, 6, 14, 14, 14, 14, 14, 14, 6, 21, 21, 21, 21, 21, 21, 21, 21, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 4, 14, 14, 14, 14, 14, 14, 14, 21, 21, 21, 21, 7] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573595 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521573595 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573595/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573595/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573595 Building ZINC001521573595 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573595' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573595 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521573595 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573595/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573595 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 688) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H](Cc2ccccc2)c2nc3ccccc3s2)cn1) `ZINC001521573595.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521573595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521573595 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H](Cc2ccccc2)c2nc3ccccc3s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 13, 13, 13, 13, 13, 13, 6, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 4, 13, 13, 13, 13, 13, 13, 13, 19, 19, 19, 19, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573595 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573595/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573595 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 689) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H](Cc2ccccc2)c2nc3ccccc3s2)cn1) `ZINC001521573595.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521573595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573595/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521573595 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H](Cc2ccccc2)c2nc3ccccc3s2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 14, 14, 7, 7, 1, 1, 1, 1, 4, 4, 4, 6, 6, 14, 14, 14, 14, 14, 14, 6, 21, 21, 21, 21, 21, 21, 21, 21, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 4, 14, 14, 14, 14, 14, 14, 14, 21, 21, 21, 21, 7] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573595 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521573595 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573595/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573595/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521573595 Building ZINC001521640133 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521640133' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521640133 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521640133 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521640133/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521640133 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/690 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CCCOc1ccccc1)C1CCOCC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001521640133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521640133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521640133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001521640133 none O=C(N(CCCOc1ccccc1)C1CCOCC1)[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', 'C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 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, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 9, 13, 44, 46, 46, 44, 46, 46, 4, 6, 6, 6, 6, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 9, 9, 13, 13, 46, 46, 44, 46, 46, 6, 6, 6, 6, 6, 6, 6, 6, 6, 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, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 124 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521640133 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521640133/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521640133 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 691) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/691 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/691' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CCCOc1ccccc1)C1CCOCC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001521640133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521640133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521640133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001521640133 none O=C(N(CCCOc1ccccc1)C1CCOCC1)[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', 'C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 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, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 10, 17, 45, 46, 46, 45, 46, 46, 6, 8, 8, 8, 8, 8, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 10, 10, 17, 17, 46, 46, 45, 46, 46, 8, 8, 8, 8, 8, 8, 8, 8, 8, 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, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 139 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521640133 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521640133 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521640133/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521640133/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521640133 Building ZINC001521640133 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521640133' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521640133 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521640133 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521640133/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521640133 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 690) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N(CCCOc1ccccc1)C1CCOCC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001521640133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521640133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521640133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001521640133 none O=C(N(CCCOc1ccccc1)C1CCOCC1)[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', 'C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 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, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 9, 13, 44, 46, 46, 44, 46, 46, 4, 6, 6, 6, 6, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 9, 9, 13, 13, 46, 46, 44, 46, 46, 6, 6, 6, 6, 6, 6, 6, 6, 6, 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, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 124 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521640133 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521640133/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521640133 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 691) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N(CCCOc1ccccc1)C1CCOCC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001521640133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521640133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521640133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001521640133 none O=C(N(CCCOc1ccccc1)C1CCOCC1)[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', 'C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 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, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 10, 17, 45, 46, 46, 45, 46, 46, 6, 8, 8, 8, 8, 8, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 10, 10, 17, 17, 46, 46, 45, 46, 46, 8, 8, 8, 8, 8, 8, 8, 8, 8, 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, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 139 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521640133 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521640133 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521640133/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521640133/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521640133 Building ZINC001521646028 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521646028' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521646028 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521646028 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521646028/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521646028 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/692 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(I)cccc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001521646028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521646028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521646028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 34 natoms 33 natoms 32 natoms 31 names: ZINC001521646028 none Cc1c(I)cccc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'I', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 18, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 10, 36, 36, 8, 8, 1, 8, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 36, 36, 36, 18, 36, 36, 8, 6, 1, 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]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521646028 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521646028/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521646028 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 693) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/693 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/693' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(I)cccc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001521646028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521646028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521646028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 34 natoms 33 natoms 32 natoms 31 names: ZINC001521646028 none Cc1c(I)cccc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'I', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 18, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 8, 8, 1, 8, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 36, 36, 36, 36, 36, 36, 8, 6, 1, 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]) total number of confs: 66 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521646028 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521646028 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521646028/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521646028/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521646028 Building ZINC001521646028 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521646028' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521646028 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521646028 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521646028/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521646028 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 692) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1c(I)cccc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001521646028.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521646028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521646028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 34 natoms 33 natoms 32 natoms 31 names: ZINC001521646028 none Cc1c(I)cccc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'I', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 18, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 10, 36, 36, 8, 8, 1, 8, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 36, 36, 36, 18, 36, 36, 8, 6, 1, 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]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521646028 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521646028/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521646028 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 693) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1c(I)cccc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001521646028.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521646028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521646028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 34 natoms 33 natoms 32 natoms 31 names: ZINC001521646028 none Cc1c(I)cccc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'I', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 18, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 8, 8, 1, 8, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 36, 36, 36, 36, 36, 36, 8, 6, 1, 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]) total number of confs: 66 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521646028 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521646028 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521646028/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521646028/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521646028 Building ZINC001521643952 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521643952' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521643952 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521643952 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521643952/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521643952 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/694 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(Oc2ccccc2C(F)(F)F)nc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001521643952.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521643952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521643952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001521643952 none O=C(NCc1ccc(Oc2ccccc2C(F)(F)F)nc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 6, 17, 17, 17, 17, 31, 32, 32, 32, 32, 32, 32, 32, 32, 32, 17, 17, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 6, 6, 17, 17, 32, 32, 32, 32, 17, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 32, 21, 22, 23] set([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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521643952 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521643952/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521643952 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 695) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/695 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/695' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(Oc2ccccc2C(F)(F)F)nc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001521643952.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521643952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521643952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001521643952 none O=C(NCc1ccc(Oc2ccccc2C(F)(F)F)nc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 6, 16, 16, 16, 16, 28, 30, 30, 30, 30, 30, 30, 30, 30, 30, 16, 16, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 6, 6, 16, 16, 30, 30, 30, 30, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 32, 21, 22, 23] set([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, 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/12845/xbi-8058088.35/working/building/ZINC001521643952 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521643952 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521643952/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521643952/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521643952 Building ZINC001521643952 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521643952' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521643952 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521643952 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521643952/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521643952 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 694) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NCc1ccc(Oc2ccccc2C(F)(F)F)nc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001521643952.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521643952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521643952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001521643952 none O=C(NCc1ccc(Oc2ccccc2C(F)(F)F)nc1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 6, 17, 17, 17, 17, 31, 32, 32, 32, 32, 32, 32, 32, 32, 32, 17, 17, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 6, 6, 17, 17, 32, 32, 32, 32, 17, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 32, 21, 22, 23] set([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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521643952 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521643952/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521643952 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 695) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NCc1ccc(Oc2ccccc2C(F)(F)F)nc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001521643952.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521643952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521643952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001521643952 none O=C(NCc1ccc(Oc2ccccc2C(F)(F)F)nc1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 6, 16, 16, 16, 16, 28, 30, 30, 30, 30, 30, 30, 30, 30, 30, 16, 16, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 6, 6, 16, 16, 30, 30, 30, 30, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 32, 21, 22, 23] set([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, 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/12845/xbi-8058088.35/working/building/ZINC001521643952 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521643952 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521643952/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521643952/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521643952 Building ZINC001521679436 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679436' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679436 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521679436 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679436/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679436 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/696 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)sc2c1CC[C@H](CC)C2) `ZINC001521679436.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521679436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001521679436 none CCOC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)sc2c1CC[C@H](CC)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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', 'S.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 14, 1, 1, 5, 5, 5, 7, 5, 5, 5, 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, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 13, 26, 7, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 19, 13, 39, 39, 39, 39, 39, 3, 7, 7, 13, 13, 13, 13, 19, 19, 19, 19, 19, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679436 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679436/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679436 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 697) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/697 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/697' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)sc2c1CC[C@H](CC)C2) `ZINC001521679436.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521679436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679436/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001521679436 none CCOC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)sc2c1CC[C@H](CC)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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', 'S.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 14, 1, 1, 5, 5, 5, 7, 5, 5, 5, 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, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 11, 26, 6, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 6, 11, 11, 11, 11, 11, 11, 11, 17, 11, 38, 38, 38, 38, 38, 2, 7, 7, 11, 11, 11, 11, 17, 17, 17, 17, 17, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679436 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521679436 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679436/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679436/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679436 Building ZINC001521679436 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679436' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679436 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521679436 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679436/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679436 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 696) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)sc2c1CC[C@H](CC)C2) `ZINC001521679436.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521679436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001521679436 none CCOC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)sc2c1CC[C@H](CC)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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', 'S.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 14, 1, 1, 5, 5, 5, 7, 5, 5, 5, 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, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 13, 26, 7, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 19, 13, 39, 39, 39, 39, 39, 3, 7, 7, 13, 13, 13, 13, 19, 19, 19, 19, 19, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679436 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679436/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679436 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 697) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)sc2c1CC[C@H](CC)C2) `ZINC001521679436.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521679436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679436/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001521679436 none CCOC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)sc2c1CC[C@H](CC)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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', 'S.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 14, 1, 1, 5, 5, 5, 7, 5, 5, 5, 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, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 11, 26, 6, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 6, 11, 11, 11, 11, 11, 11, 11, 17, 11, 38, 38, 38, 38, 38, 2, 7, 7, 11, 11, 11, 11, 17, 17, 17, 17, 17, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679436 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521679436 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679436/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679436/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679436 Building ZINC001521679438 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679438' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679438 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521679438 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679438/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679438 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/698 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)sc2c1CC[C@@H](CC)C2) `ZINC001521679438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521679438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001521679438 none CCOC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)sc2c1CC[C@@H](CC)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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', 'S.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 14, 1, 1, 5, 5, 5, 7, 5, 5, 5, 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, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 16, 16, 6, 16, 6, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 6, 11, 6, 11, 11, 11, 11, 11, 17, 11, 32, 32, 32, 32, 32, 2, 7, 7, 11, 11, 11, 11, 17, 17, 17, 17, 17, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679438 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679438/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679438 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 699) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/699 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/699' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)sc2c1CC[C@@H](CC)C2) `ZINC001521679438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521679438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001521679438 none CCOC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)sc2c1CC[C@@H](CC)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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', 'S.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 14, 1, 1, 5, 5, 5, 7, 5, 5, 5, 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, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 17, 7, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 13, 7, 13, 13, 13, 13, 13, 19, 13, 31, 31, 31, 31, 31, 3, 7, 7, 13, 13, 13, 13, 19, 19, 19, 19, 19, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679438 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521679438 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679438/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679438/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679438 Building ZINC001521679438 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679438' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679438 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521679438 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679438/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679438 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 698) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)sc2c1CC[C@@H](CC)C2) `ZINC001521679438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521679438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001521679438 none CCOC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)sc2c1CC[C@@H](CC)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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', 'S.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 14, 1, 1, 5, 5, 5, 7, 5, 5, 5, 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, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 16, 16, 6, 16, 6, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 6, 11, 6, 11, 11, 11, 11, 11, 17, 11, 32, 32, 32, 32, 32, 2, 7, 7, 11, 11, 11, 11, 17, 17, 17, 17, 17, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679438 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679438/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679438 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 699) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)sc2c1CC[C@@H](CC)C2) `ZINC001521679438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521679438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001521679438 none CCOC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)sc2c1CC[C@@H](CC)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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', 'S.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 14, 1, 1, 5, 5, 5, 7, 5, 5, 5, 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, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 17, 7, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 13, 7, 13, 13, 13, 13, 13, 19, 13, 31, 31, 31, 31, 31, 3, 7, 7, 13, 13, 13, 13, 19, 19, 19, 19, 19, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679438 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521679438 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679438/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679438/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521679438 Building ZINC001521696717 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696717' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696717 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521696717 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696717/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696717 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/700 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/700' -> `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]1CCc2ccccc21) `ZINC001521696717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521696717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001521696717 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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', '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, 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, 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] dock color type numbers: [7, 7, 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, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 15, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 8, 8, 3, 8, 2, 2, 2, 2, 12, 12, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696717 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696717/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696717 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 701) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/701 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/701' -> `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]1CCc2ccccc21) `ZINC001521696717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521696717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001521696717 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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', '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, 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, 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] dock color type numbers: [7, 7, 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, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 15, 16, 16, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696717 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521696717 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696717/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696717/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696717 Building ZINC001521696717 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696717' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696717 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521696717 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696717/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696717 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 700) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCc2ccccc21) `ZINC001521696717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521696717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001521696717 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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', '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, 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, 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] dock color type numbers: [7, 7, 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, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 15, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 8, 8, 3, 8, 2, 2, 2, 2, 12, 12, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696717 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696717/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696717 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 701) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCc2ccccc21) `ZINC001521696717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521696717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001521696717 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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', '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, 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, 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] dock color type numbers: [7, 7, 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, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 15, 16, 16, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696717 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521696717 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696717/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696717/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696717 Building ZINC001521696718 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696718' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696718 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521696718 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696718/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696718 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/702 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/702' -> `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]1CCc2ccccc21) `ZINC001521696718.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521696718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001521696718 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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', '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, 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, 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] dock color type numbers: [7, 7, 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, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 14, 16, 16, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 10, 10, 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696718 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696718/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696718 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 703) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/703 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/703' -> `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]1CCc2ccccc21) `ZINC001521696718.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521696718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696718/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001521696718 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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', '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, 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, 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] dock color type numbers: [7, 7, 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, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 9, 9, 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696718 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521696718 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696718/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696718/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696718 Building ZINC001521696718 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696718' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696718 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521696718 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696718/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696718 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 702) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCc2ccccc21) `ZINC001521696718.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521696718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001521696718 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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', '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, 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, 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] dock color type numbers: [7, 7, 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, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 14, 16, 16, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 10, 10, 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696718 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696718/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696718 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 703) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCc2ccccc21) `ZINC001521696718.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521696718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696718/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001521696718 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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', '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, 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, 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] dock color type numbers: [7, 7, 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, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 9, 9, 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696718 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521696718 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696718/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696718/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521696718 Building ZINC001521730836 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730836' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730836 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521730836 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730836/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730836 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/704 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2cc(F)cc(Br)c2)cc1Cl) `ZINC001521730836.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521730836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001521730836 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2cc(F)cc(Br)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', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 5, 7, 1, 1, 1, 15, 1, 1, 17, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 20, 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: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730836 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730836/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730836 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 705) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/705 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/705' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2cc(F)cc(Br)c2)cc1Cl) `ZINC001521730836.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521730836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730836/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001521730836 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2cc(F)cc(Br)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', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 5, 7, 1, 1, 1, 15, 1, 1, 17, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 8, 8, 8, 8, 8, 8, 26, 26, 26, 25, 26, 26, 26, 4, 4, 4, 9, 9, 9, 4, 4, 8, 8, 8, 8, 8, 8, 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730836 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521730836 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730836/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730836/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730836 Building ZINC001521730836 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730836' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730836 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521730836 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730836/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730836 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 704) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/704: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2cc(F)cc(Br)c2)cc1Cl) `ZINC001521730836.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521730836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001521730836 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2cc(F)cc(Br)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', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 5, 7, 1, 1, 1, 15, 1, 1, 17, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 20, 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: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730836 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730836/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730836 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 705) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/705: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2cc(F)cc(Br)c2)cc1Cl) `ZINC001521730836.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521730836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730836/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001521730836 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2cc(F)cc(Br)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', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 5, 7, 1, 1, 1, 15, 1, 1, 17, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 8, 8, 8, 8, 8, 8, 26, 26, 26, 25, 26, 26, 26, 4, 4, 4, 9, 9, 9, 4, 4, 8, 8, 8, 8, 8, 8, 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]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730836 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521730836 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730836/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730836/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730836 Building ZINC001521730837 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730837' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730837 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521730837 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730837/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730837 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/706 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2cc(F)cc(Br)c2)cc1Cl) `ZINC001521730837.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521730837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001521730837 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2cc(F)cc(Br)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', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 5, 7, 1, 1, 1, 15, 1, 1, 17, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 4, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 9, 26, 26, 26, 17, 26, 26, 26, 4, 4, 4, 11, 11, 11, 4, 4, 9, 9, 9, 9, 9, 9, 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730837 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730837/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730837 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 707) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/707 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/707' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2cc(F)cc(Br)c2)cc1Cl) `ZINC001521730837.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521730837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001521730837 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2cc(F)cc(Br)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', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 5, 7, 1, 1, 1, 15, 1, 1, 17, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 21, 21, 21, 17, 21, 21, 21, 4, 4, 4, 9, 9, 9, 4, 4, 5, 5, 5, 5, 5, 5, 21, 21, 21, 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: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730837 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521730837 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730837/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730837/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730837 Building ZINC001521730837 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730837' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730837 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521730837 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730837/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730837 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 706) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2cc(F)cc(Br)c2)cc1Cl) `ZINC001521730837.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521730837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001521730837 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2cc(F)cc(Br)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', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 5, 7, 1, 1, 1, 15, 1, 1, 17, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 4, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 9, 26, 26, 26, 17, 26, 26, 26, 4, 4, 4, 11, 11, 11, 4, 4, 9, 9, 9, 9, 9, 9, 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730837 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730837/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730837 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 707) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2cc(F)cc(Br)c2)cc1Cl) `ZINC001521730837.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521730837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001521730837 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2cc(F)cc(Br)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', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 5, 7, 1, 1, 1, 15, 1, 1, 17, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 21, 21, 21, 17, 21, 21, 21, 4, 4, 4, 9, 9, 9, 4, 4, 5, 5, 5, 5, 5, 5, 21, 21, 21, 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: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730837 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521730837 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730837/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730837/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521730837 Building ZINC001521733564 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001521733564 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/708 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@]([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1) `ZINC001521733564.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521733564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521733564 none C[C@H]1CC[N@]([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 29, 15, 25, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 25, 34, 34, 34, 34, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 4, 3, 1, 3, 34, 34, 34, 33, 33, 33, 33] 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: 134 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 709) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/709 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/709' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@@]([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1) `ZINC001521733564.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521733564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521733564 none C[C@H]1CC[N@@]([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 29, 15, 25, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 25, 34, 34, 34, 34, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 4, 3, 1, 3, 34, 34, 34, 33, 33, 33, 33] 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: 137 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 710) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/710 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/710' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@]([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1) `ZINC001521733564.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001521733564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521733564 none C[C@H]1CC[N@]([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 28, 14, 24, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 38, 38, 38, 38, 36, 36, 36, 36, 36, 36, 36, 36, 36, 14, 14, 3, 3, 1, 3, 38, 38, 38, 36, 36, 36, 36] 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: 147 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 711) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/711 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/711' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@@]([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1) `ZINC001521733564.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001521733564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521733564 none C[C@H]1CC[N@@]([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 35, 28, 14, 24, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 37, 37, 37, 37, 35, 35, 35, 35, 35, 35, 35, 35, 35, 14, 14, 3, 3, 1, 3, 37, 37, 37, 35, 35, 35, 35] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 143 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521733564 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 Building ZINC001521733564 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001521733564 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 708) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@H]1CC[N@]([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1) `ZINC001521733564.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521733564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521733564 none C[C@H]1CC[N@]([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 29, 15, 25, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 25, 34, 34, 34, 34, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 4, 3, 1, 3, 34, 34, 34, 33, 33, 33, 33] 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: 134 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 709) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@H]1CC[N@@]([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1) `ZINC001521733564.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521733564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521733564 none C[C@H]1CC[N@@]([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 29, 15, 25, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 25, 34, 34, 34, 34, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 4, 3, 1, 3, 34, 34, 34, 33, 33, 33, 33] 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: 137 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 710) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/710: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@]([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1) `ZINC001521733564.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001521733564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521733564 none C[C@H]1CC[N@]([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 28, 14, 24, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 38, 38, 38, 38, 36, 36, 36, 36, 36, 36, 36, 36, 36, 14, 14, 3, 3, 1, 3, 38, 38, 38, 36, 36, 36, 36] 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: 147 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 711) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/711: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@@]([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1) `ZINC001521733564.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001521733564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521733564 none C[C@H]1CC[N@@]([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 35, 28, 14, 24, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 37, 37, 37, 37, 35, 35, 35, 35, 35, 35, 35, 35, 35, 14, 14, 3, 3, 1, 3, 37, 37, 37, 35, 35, 35, 35] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 143 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521733564 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 Building ZINC001521733564 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001521733564 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 708) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@H]1CC[N@]([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1) `ZINC001521733564.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521733564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521733564 none C[C@H]1CC[N@]([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 29, 15, 25, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 25, 34, 34, 34, 34, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 4, 3, 1, 3, 34, 34, 34, 33, 33, 33, 33] 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: 134 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 709) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@H]1CC[N@@]([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1) `ZINC001521733564.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521733564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521733564 none C[C@H]1CC[N@@]([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 29, 15, 25, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 25, 34, 34, 34, 34, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 4, 3, 1, 3, 34, 34, 34, 33, 33, 33, 33] 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: 137 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 710) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/710: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@]([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1) `ZINC001521733564.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001521733564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521733564 none C[C@H]1CC[N@]([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 28, 14, 24, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 38, 38, 38, 38, 36, 36, 36, 36, 36, 36, 36, 36, 36, 14, 14, 3, 3, 1, 3, 38, 38, 38, 36, 36, 36, 36] 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: 147 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 711) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/711: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@@]([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1) `ZINC001521733564.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001521733564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521733564 none C[C@H]1CC[N@@]([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 35, 28, 14, 24, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 37, 37, 37, 37, 35, 35, 35, 35, 35, 35, 35, 35, 35, 14, 14, 3, 3, 1, 3, 37, 37, 37, 35, 35, 35, 35] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 143 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521733564 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 Building ZINC001521733564 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001521733564 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 708) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@H]1CC[N@]([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1) `ZINC001521733564.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521733564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521733564 none C[C@H]1CC[N@]([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 29, 15, 25, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 25, 34, 34, 34, 34, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 4, 3, 1, 3, 34, 34, 34, 33, 33, 33, 33] 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: 134 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 709) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@H]1CC[N@@]([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1) `ZINC001521733564.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521733564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521733564 none C[C@H]1CC[N@@]([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 29, 15, 25, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 25, 34, 34, 34, 34, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 4, 3, 1, 3, 34, 34, 34, 33, 33, 33, 33] 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: 137 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 710) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/710: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@]([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1) `ZINC001521733564.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001521733564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521733564 none C[C@H]1CC[N@]([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 28, 14, 24, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 38, 38, 38, 38, 36, 36, 36, 36, 36, 36, 36, 36, 36, 14, 14, 3, 3, 1, 3, 38, 38, 38, 36, 36, 36, 36] 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: 147 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 711) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/711: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@@]([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1) `ZINC001521733564.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001521733564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521733564 none C[C@H]1CC[N@@]([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 35, 28, 14, 24, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 24, 37, 37, 37, 37, 35, 35, 35, 35, 35, 35, 35, 35, 35, 14, 14, 3, 3, 1, 3, 37, 37, 37, 35, 35, 35, 35] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 143 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521733564 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733564 Building ZINC001521733565 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001521733565 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/712 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@]([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1) `ZINC001521733565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521733565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521733565 none C[C@H]1CC[N@]([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 27, 14, 23, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 23, 36, 36, 36, 36, 33, 33, 33, 33, 33, 33, 33, 33, 33, 14, 14, 3, 3, 1, 3, 36, 36, 36, 33, 33, 33, 33] 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: 137 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 713) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/713 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/713' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@@]([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1) `ZINC001521733565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521733565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521733565 none C[C@H]1CC[N@@]([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 27, 14, 23, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 23, 36, 36, 36, 36, 33, 33, 33, 33, 33, 33, 33, 33, 33, 14, 14, 3, 3, 1, 3, 36, 36, 36, 33, 33, 33, 33] 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: 137 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 714) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/714 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/714' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@]([C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1) `ZINC001521733565.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001521733565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521733565 none C[C@H]1CC[N@]([C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 26, 16, 25, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 25, 39, 39, 39, 39, 36, 36, 36, 36, 36, 36, 36, 36, 36, 16, 16, 4, 3, 1, 3, 39, 39, 39, 36, 36, 36, 36] 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: 145 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 715) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/715 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/715' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@@]([C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1) `ZINC001521733565.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001521733565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521733565 none C[C@H]1CC[N@@]([C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 26, 16, 25, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 25, 39, 39, 39, 39, 36, 36, 36, 36, 36, 36, 36, 36, 36, 16, 16, 4, 3, 1, 3, 39, 39, 39, 36, 36, 36, 36] 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: 145 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521733565 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 Building ZINC001521733565 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001521733565 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 712) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@H]1CC[N@]([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1) `ZINC001521733565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521733565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521733565 none C[C@H]1CC[N@]([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 27, 14, 23, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 23, 36, 36, 36, 36, 33, 33, 33, 33, 33, 33, 33, 33, 33, 14, 14, 3, 3, 1, 3, 36, 36, 36, 33, 33, 33, 33] 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: 137 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 713) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@H]1CC[N@@]([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1) `ZINC001521733565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521733565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521733565 none C[C@H]1CC[N@@]([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 27, 14, 23, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 23, 36, 36, 36, 36, 33, 33, 33, 33, 33, 33, 33, 33, 33, 14, 14, 3, 3, 1, 3, 36, 36, 36, 33, 33, 33, 33] 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: 137 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 714) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/714: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@]([C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1) `ZINC001521733565.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001521733565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521733565 none C[C@H]1CC[N@]([C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 26, 16, 25, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 25, 39, 39, 39, 39, 36, 36, 36, 36, 36, 36, 36, 36, 36, 16, 16, 4, 3, 1, 3, 39, 39, 39, 36, 36, 36, 36] 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: 145 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 715) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/715: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@@]([C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1) `ZINC001521733565.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001521733565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521733565 none C[C@H]1CC[N@@]([C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 26, 16, 25, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 25, 39, 39, 39, 39, 36, 36, 36, 36, 36, 36, 36, 36, 36, 16, 16, 4, 3, 1, 3, 39, 39, 39, 36, 36, 36, 36] 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: 145 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521733565 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 Building ZINC001521733565 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001521733565 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 712) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@H]1CC[N@]([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1) `ZINC001521733565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521733565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521733565 none C[C@H]1CC[N@]([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 27, 14, 23, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 23, 36, 36, 36, 36, 33, 33, 33, 33, 33, 33, 33, 33, 33, 14, 14, 3, 3, 1, 3, 36, 36, 36, 33, 33, 33, 33] 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: 137 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 713) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@H]1CC[N@@]([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1) `ZINC001521733565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521733565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521733565 none C[C@H]1CC[N@@]([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 27, 14, 23, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 23, 36, 36, 36, 36, 33, 33, 33, 33, 33, 33, 33, 33, 33, 14, 14, 3, 3, 1, 3, 36, 36, 36, 33, 33, 33, 33] 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: 137 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 714) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/714: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@]([C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1) `ZINC001521733565.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001521733565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521733565 none C[C@H]1CC[N@]([C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 26, 16, 25, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 25, 39, 39, 39, 39, 36, 36, 36, 36, 36, 36, 36, 36, 36, 16, 16, 4, 3, 1, 3, 39, 39, 39, 36, 36, 36, 36] 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: 145 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 715) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/715: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@@]([C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1) `ZINC001521733565.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001521733565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521733565 none C[C@H]1CC[N@@]([C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 26, 16, 25, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 25, 39, 39, 39, 39, 36, 36, 36, 36, 36, 36, 36, 36, 36, 16, 16, 4, 3, 1, 3, 39, 39, 39, 36, 36, 36, 36] 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: 145 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521733565 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 Building ZINC001521733565 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001521733565 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 712) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@H]1CC[N@]([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1) `ZINC001521733565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521733565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521733565 none C[C@H]1CC[N@]([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 27, 14, 23, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 23, 36, 36, 36, 36, 33, 33, 33, 33, 33, 33, 33, 33, 33, 14, 14, 3, 3, 1, 3, 36, 36, 36, 33, 33, 33, 33] 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: 137 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 713) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@H]1CC[N@@]([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1) `ZINC001521733565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521733565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521733565 none C[C@H]1CC[N@@]([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 27, 14, 23, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 23, 36, 36, 36, 36, 33, 33, 33, 33, 33, 33, 33, 33, 33, 14, 14, 3, 3, 1, 3, 36, 36, 36, 33, 33, 33, 33] 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: 137 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 714) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/714: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@]([C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1) `ZINC001521733565.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001521733565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521733565 none C[C@H]1CC[N@]([C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 26, 16, 25, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 25, 39, 39, 39, 39, 36, 36, 36, 36, 36, 36, 36, 36, 36, 16, 16, 4, 3, 1, 3, 39, 39, 39, 36, 36, 36, 36] 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: 145 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 715) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/715: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[N@@]([C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1) `ZINC001521733565.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001521733565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521733565 none C[C@H]1CC[N@@]([C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c2cccs2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.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.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 26, 16, 25, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 25, 39, 39, 39, 39, 36, 36, 36, 36, 36, 36, 36, 36, 36, 16, 16, 4, 3, 1, 3, 39, 39, 39, 36, 36, 36, 36] 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: 145 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521733565 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521733565 Building ZINC001521737703 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521737703' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521737703 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521737703 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521737703/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521737703 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/716 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(CS(=O)(=O)c2ccccc2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001521737703.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521737703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521737703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001521737703 none O=C(Nc1cccc(CS(=O)(=O)c2ccccc2)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', 'C.3', 'S.o2', 'O.2', 'O.2', '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', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 11, 1, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 3, 16, 16, 27, 47, 47, 47, 47, 47, 47, 47, 47, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 16, 16, 3, 27, 27, 47, 47, 47, 47, 47, 16, 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, 43]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521737703 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521737703/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521737703 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 717) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/717 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/717' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(CS(=O)(=O)c2ccccc2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001521737703.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521737703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521737703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001521737703 none O=C(Nc1cccc(CS(=O)(=O)c2ccccc2)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', 'C.3', 'S.o2', 'O.2', 'O.2', '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', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 11, 1, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 3, 16, 16, 26, 46, 46, 46, 46, 46, 46, 46, 46, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 16, 16, 3, 26, 26, 46, 46, 46, 46, 46, 16, 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, 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/12845/xbi-8058088.35/working/building/ZINC001521737703 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521737703 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521737703/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521737703/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521737703 Building ZINC001521737703 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521737703' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521737703 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521737703 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521737703/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521737703 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 716) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1cccc(CS(=O)(=O)c2ccccc2)c1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001521737703.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521737703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521737703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001521737703 none O=C(Nc1cccc(CS(=O)(=O)c2ccccc2)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', 'C.3', 'S.o2', 'O.2', 'O.2', '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', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 11, 1, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 3, 16, 16, 27, 47, 47, 47, 47, 47, 47, 47, 47, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 16, 16, 3, 27, 27, 47, 47, 47, 47, 47, 16, 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, 43]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521737703 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521737703/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521737703 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 717) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1cccc(CS(=O)(=O)c2ccccc2)c1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001521737703.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521737703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521737703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001521737703 none O=C(Nc1cccc(CS(=O)(=O)c2ccccc2)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', 'C.3', 'S.o2', 'O.2', 'O.2', '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', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 11, 1, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 3, 16, 16, 26, 46, 46, 46, 46, 46, 46, 46, 46, 16, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 16, 16, 3, 26, 26, 46, 46, 46, 46, 46, 16, 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, 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/12845/xbi-8058088.35/working/building/ZINC001521737703 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521737703 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521737703/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521737703/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521737703 Building ZINC001521738560 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521738560' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521738560 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521738560 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521738560/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521738560 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/718 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(OCc2ccc(Cl)cc2)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001521738560.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521738560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521738560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521738560 none O=C(Nc1cccc(OCc2ccc(Cl)cc2)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 16, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 13, 13, 13, 13, 13, 16, 16, 27, 27, 27, 27, 27, 27, 13, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 13, 13, 13, 16, 16, 27, 27, 27, 27, 13, 7, 7, 7, 7, 7, 7, 7] 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: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521738560 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521738560/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521738560 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 719) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/719 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/719' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(OCc2ccc(Cl)cc2)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001521738560.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521738560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521738560/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521738560 none O=C(Nc1cccc(OCc2ccc(Cl)cc2)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 16, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 13, 13, 13, 13, 13, 15, 15, 25, 25, 25, 25, 25, 25, 13, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 13, 13, 13, 15, 15, 25, 25, 25, 25, 13, 7, 7, 7, 7, 7, 7, 7] 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: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521738560 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521738560 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521738560/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521738560/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521738560 Building ZINC001521738560 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521738560' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521738560 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521738560 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521738560/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521738560 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 718) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1cccc(OCc2ccc(Cl)cc2)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001521738560.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521738560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521738560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521738560 none O=C(Nc1cccc(OCc2ccc(Cl)cc2)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 16, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 13, 13, 13, 13, 13, 16, 16, 27, 27, 27, 27, 27, 27, 13, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 13, 13, 13, 16, 16, 27, 27, 27, 27, 13, 7, 7, 7, 7, 7, 7, 7] 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: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521738560 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521738560/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521738560 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 719) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1cccc(OCc2ccc(Cl)cc2)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001521738560.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521738560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521738560/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521738560 none O=C(Nc1cccc(OCc2ccc(Cl)cc2)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 16, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 13, 13, 13, 13, 13, 15, 15, 25, 25, 25, 25, 25, 25, 13, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 13, 13, 13, 15, 15, 25, 25, 25, 25, 13, 7, 7, 7, 7, 7, 7, 7] 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: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521738560 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521738560 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521738560/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521738560/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521738560 Building ZINC001521776219 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521776219' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521776219 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521776219 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521776219/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521776219 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/720 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CCc1ccccc1)Cc1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001521776219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521776219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521776219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521776219 none O=C(N(CCc1ccccc1)Cc1ccccc1)[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.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7] 0 hydrogens need 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, 13, 13, 15, 15, 13, 15, 15, 7, 18, 22, 22, 20, 22, 22, 1, 1, 1, 4, 4, 4, 4, 4, 13, 13, 13, 13, 15, 15, 15, 15, 15, 18, 18, 22, 22, 22, 22, 22, 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]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521776219 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521776219/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521776219 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 721) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/721 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/721' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CCc1ccccc1)Cc1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001521776219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521776219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521776219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521776219 none O=C(N(CCc1ccccc1)Cc1ccccc1)[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.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7] 0 hydrogens need 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, 13, 13, 15, 15, 15, 15, 15, 7, 18, 22, 22, 22, 22, 22, 1, 1, 1, 4, 4, 4, 4, 4, 13, 13, 13, 13, 15, 15, 15, 15, 15, 18, 18, 22, 22, 22, 22, 22, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521776219 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521776219 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521776219/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521776219/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521776219 Building ZINC001521776219 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521776219' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521776219 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521776219 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521776219/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521776219 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 720) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N(CCc1ccccc1)Cc1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001521776219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521776219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521776219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521776219 none O=C(N(CCc1ccccc1)Cc1ccccc1)[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.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7] 0 hydrogens need 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, 13, 13, 15, 15, 13, 15, 15, 7, 18, 22, 22, 20, 22, 22, 1, 1, 1, 4, 4, 4, 4, 4, 13, 13, 13, 13, 15, 15, 15, 15, 15, 18, 18, 22, 22, 22, 22, 22, 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]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521776219 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521776219/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521776219 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 721) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N(CCc1ccccc1)Cc1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001521776219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521776219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521776219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521776219 none O=C(N(CCc1ccccc1)Cc1ccccc1)[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.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7] 0 hydrogens need 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, 13, 13, 15, 15, 15, 15, 15, 7, 18, 22, 22, 22, 22, 22, 1, 1, 1, 4, 4, 4, 4, 4, 13, 13, 13, 13, 15, 15, 15, 15, 15, 18, 18, 22, 22, 22, 22, 22, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521776219 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521776219 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521776219/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521776219/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521776219 Building ZINC001521818699 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521818699' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521818699 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521818699 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521818699/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521818699 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/722 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2cccc(F)c2F)CCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001521818699.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521818699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521818699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001521818699 none O=C(NCC1(c2cccc(F)c2F)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', 'C.ar', 'F', '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, 1, 1, 1, 15, 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, 23, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 7, 7, 7, 7, 7, 4, 15, 15, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 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: 113 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521818699 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521818699/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521818699 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 723) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/723 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/723' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2cccc(F)c2F)CCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001521818699.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521818699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521818699/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001521818699 none O=C(NCC1(c2cccc(F)c2F)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', 'C.ar', 'F', '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, 1, 1, 1, 15, 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, 19, 34, 35, 35, 35, 35, 35, 35, 35, 34, 34, 34, 34, 1, 1, 1, 6, 6, 6, 6, 6, 3, 13, 13, 35, 35, 35, 34, 34, 34, 34, 34, 34, 34, 34, 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]) total number of confs: 103 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521818699 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521818699 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521818699/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521818699/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521818699 Building ZINC001521818699 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521818699' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521818699 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521818699 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521818699/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521818699 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 722) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NCC1(c2cccc(F)c2F)CCCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001521818699.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521818699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521818699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001521818699 none O=C(NCC1(c2cccc(F)c2F)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', 'C.ar', 'F', '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, 1, 1, 1, 15, 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, 23, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 7, 7, 7, 7, 7, 4, 15, 15, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 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: 113 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521818699 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521818699/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521818699 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 723) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NCC1(c2cccc(F)c2F)CCCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001521818699.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521818699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521818699/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001521818699 none O=C(NCC1(c2cccc(F)c2F)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', 'C.ar', 'F', '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, 1, 1, 1, 15, 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, 19, 34, 35, 35, 35, 35, 35, 35, 35, 34, 34, 34, 34, 1, 1, 1, 6, 6, 6, 6, 6, 3, 13, 13, 35, 35, 35, 34, 34, 34, 34, 34, 34, 34, 34, 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]) total number of confs: 103 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521818699 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521818699 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521818699/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521818699/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521818699 Building ZINC001521876021 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876021' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876021 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521876021 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876021/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876021 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/724 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CC(F)(F)F)c2cccc(C(F)(F)F)c2)cn1) `ZINC001521876021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521876021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521876021 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CC(F)(F)F)c2cccc(C(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 10, 10, 8, 8, 1, 1, 1, 1, 4, 4, 4, 7, 7, 9, 9, 9, 9, 7, 16, 16, 13, 16, 16, 16, 16, 16, 16, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 4, 9, 9, 16, 16, 13, 16, 8] 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]) total number of confs: 83 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876021 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876021/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876021 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 725) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/725 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/725' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CC(F)(F)F)c2cccc(C(F)(F)F)c2)cn1) `ZINC001521876021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521876021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521876021 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CC(F)(F)F)c2cccc(C(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 7, 7, 1, 1, 1, 1, 4, 4, 4, 7, 7, 9, 9, 9, 9, 7, 15, 15, 13, 15, 15, 15, 15, 15, 15, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 4, 9, 9, 15, 15, 13, 15, 7] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876021 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521876021 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876021/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876021/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876021 Building ZINC001521876021 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876021' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876021 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521876021 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876021/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876021 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 724) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/724: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CC(F)(F)F)c2cccc(C(F)(F)F)c2)cn1) `ZINC001521876021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521876021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521876021 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CC(F)(F)F)c2cccc(C(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 10, 10, 8, 8, 1, 1, 1, 1, 4, 4, 4, 7, 7, 9, 9, 9, 9, 7, 16, 16, 13, 16, 16, 16, 16, 16, 16, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 4, 9, 9, 16, 16, 13, 16, 8] 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]) total number of confs: 83 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876021 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876021/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876021 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 725) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/725: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CC(F)(F)F)c2cccc(C(F)(F)F)c2)cn1) `ZINC001521876021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521876021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521876021 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CC(F)(F)F)c2cccc(C(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 7, 7, 1, 1, 1, 1, 4, 4, 4, 7, 7, 9, 9, 9, 9, 7, 15, 15, 13, 15, 15, 15, 15, 15, 15, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 4, 9, 9, 15, 15, 13, 15, 7] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876021 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521876021 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876021/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876021/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876021 Building ZINC001521876022 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876022' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876022 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521876022 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876022/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876022 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/726 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CC(F)(F)F)c2cccc(C(F)(F)F)c2)cn1) `ZINC001521876022.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521876022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521876022 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CC(F)(F)F)c2cccc(C(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 9, 9, 7, 7, 1, 1, 1, 1, 4, 4, 4, 7, 7, 9, 9, 9, 9, 7, 15, 15, 13, 15, 15, 15, 15, 15, 15, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 4, 9, 9, 15, 15, 13, 15, 7] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876022 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876022/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876022 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 727) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/727 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/727' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H](CC(F)(F)F)c2cccc(C(F)(F)F)c2)cn1) `ZINC001521876022.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521876022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521876022 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H](CC(F)(F)F)c2cccc(C(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 7, 7, 1, 1, 1, 1, 4, 4, 4, 7, 7, 9, 9, 9, 9, 7, 17, 17, 14, 17, 17, 17, 17, 17, 17, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 4, 9, 9, 17, 17, 14, 17, 7] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 93 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876022 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521876022 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876022/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876022/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876022 Building ZINC001521876022 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876022' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876022 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521876022 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876022/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876022 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 726) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CC(F)(F)F)c2cccc(C(F)(F)F)c2)cn1) `ZINC001521876022.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521876022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521876022 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CC(F)(F)F)c2cccc(C(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 9, 9, 7, 7, 1, 1, 1, 1, 4, 4, 4, 7, 7, 9, 9, 9, 9, 7, 15, 15, 13, 15, 15, 15, 15, 15, 15, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 4, 9, 9, 15, 15, 13, 15, 7] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876022 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876022/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876022 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 727) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H](CC(F)(F)F)c2cccc(C(F)(F)F)c2)cn1) `ZINC001521876022.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521876022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521876022 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H](CC(F)(F)F)c2cccc(C(F)(F)F)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 15, 15, 15, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 7, 7, 1, 1, 1, 1, 4, 4, 4, 7, 7, 9, 9, 9, 9, 7, 17, 17, 14, 17, 17, 17, 17, 17, 17, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 4, 9, 9, 17, 17, 14, 17, 7] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 93 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876022 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521876022 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876022/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876022/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521876022 Building ZINC001521889116 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889116' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889116 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521889116 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889116/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889116 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/728 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](c1ccc(Cl)cc1Cl)N(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)C1CC1) `ZINC001521889116.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521889116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521889116 none CCOC(=O)[C@H](c1ccc(Cl)cc1Cl)N(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)C1CC1 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', 'Cl', '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.3', '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, 5, 7, 1, 1, 1, 1, 16, 1, 1, 16, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [38, 27, 27, 9, 27, 6, 9, 9, 16, 16, 9, 10, 16, 16, 16, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 16, 16, 38, 38, 38, 38, 38, 16, 16, 16, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 16] 46 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: 214 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889116 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889116/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889116 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 729) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/729 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/729' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](c1ccc(Cl)cc1Cl)N(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)C1CC1) `ZINC001521889116.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521889116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889116/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521889116 none CCOC(=O)[C@H](c1ccc(Cl)cc1Cl)N(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)C1CC1 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', 'Cl', '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.3', '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, 5, 7, 1, 1, 1, 1, 16, 1, 1, 16, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 11, 39, 7, 11, 11, 17, 17, 11, 11, 17, 17, 17, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 12, 12, 48, 48, 48, 48, 48, 17, 17, 17, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12] 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: 215 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889116 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521889116 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889116/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889116/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889116 Building ZINC001521889116 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889116' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889116 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521889116 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889116/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889116 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 728) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOC(=O)[C@H](c1ccc(Cl)cc1Cl)N(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)C1CC1) `ZINC001521889116.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521889116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521889116 none CCOC(=O)[C@H](c1ccc(Cl)cc1Cl)N(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)C1CC1 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', 'Cl', '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.3', '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, 5, 7, 1, 1, 1, 1, 16, 1, 1, 16, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [38, 27, 27, 9, 27, 6, 9, 9, 16, 16, 9, 10, 16, 16, 16, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 6, 16, 16, 38, 38, 38, 38, 38, 16, 16, 16, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 16] 46 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: 214 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889116 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889116/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889116 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 729) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOC(=O)[C@H](c1ccc(Cl)cc1Cl)N(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)C1CC1) `ZINC001521889116.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521889116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889116/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521889116 none CCOC(=O)[C@H](c1ccc(Cl)cc1Cl)N(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)C1CC1 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', 'Cl', '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.3', '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, 5, 7, 1, 1, 1, 1, 16, 1, 1, 16, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 11, 39, 7, 11, 11, 17, 17, 11, 11, 17, 17, 17, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 12, 12, 48, 48, 48, 48, 48, 17, 17, 17, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12] 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: 215 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889116 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521889116 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889116/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889116/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889116 Building ZINC001521889118 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889118' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889118 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521889118 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889118/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889118 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/730 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](c1ccc(Cl)cc1Cl)N(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)C1CC1) `ZINC001521889118.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521889118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521889118 none CCOC(=O)[C@@H](c1ccc(Cl)cc1Cl)N(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)C1CC1 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', 'Cl', '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.3', '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, 5, 7, 1, 1, 1, 1, 16, 1, 1, 16, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 40, 40, 12, 40, 7, 12, 12, 18, 18, 12, 12, 18, 18, 18, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 12, 12, 48, 48, 48, 48, 48, 18, 18, 18, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12] 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: 212 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889118 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889118/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889118 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 731) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/731 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/731' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](c1ccc(Cl)cc1Cl)N(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)C1CC1) `ZINC001521889118.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521889118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521889118 none CCOC(=O)[C@@H](c1ccc(Cl)cc1Cl)N(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)C1CC1 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', 'Cl', '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.3', '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, 5, 7, 1, 1, 1, 1, 16, 1, 1, 16, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 10, 26, 7, 10, 10, 17, 17, 11, 11, 17, 17, 17, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 7, 19, 19, 41, 41, 41, 41, 41, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 19, 19, 19, 19, 19] 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: 219 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889118 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521889118 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889118/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889118/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889118 Building ZINC001521889118 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889118' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889118 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521889118 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889118/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889118 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 730) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOC(=O)[C@@H](c1ccc(Cl)cc1Cl)N(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)C1CC1) `ZINC001521889118.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521889118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521889118 none CCOC(=O)[C@@H](c1ccc(Cl)cc1Cl)N(C(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1)C1CC1 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', 'Cl', '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.3', '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, 5, 7, 1, 1, 1, 1, 16, 1, 1, 16, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 40, 40, 12, 40, 7, 12, 12, 18, 18, 12, 12, 18, 18, 18, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 12, 12, 48, 48, 48, 48, 48, 18, 18, 18, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12] 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: 212 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889118 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889118/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889118 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 731) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOC(=O)[C@@H](c1ccc(Cl)cc1Cl)N(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)C1CC1) `ZINC001521889118.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521889118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521889118 none CCOC(=O)[C@@H](c1ccc(Cl)cc1Cl)N(C(=O)[C@]([O-])([SiH3])c1ccc(C)cc1)C1CC1 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', 'Cl', '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.3', '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, 5, 7, 1, 1, 1, 1, 16, 1, 1, 16, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 10, 26, 7, 10, 10, 17, 17, 11, 11, 17, 17, 17, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 7, 19, 19, 41, 41, 41, 41, 41, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 19, 19, 19, 19, 19] 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: 219 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889118 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521889118 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889118/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889118/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521889118 Building ZINC001521895016 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895016' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895016 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521895016 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895016/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895016 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/732 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](c1ccc(Cl)cc1Cl)N(C(=O)[C@@]([O-])([SiH3])c1cccc(C)c1)C1CC1) `ZINC001521895016.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521895016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521895016 none CCOC(=O)[C@H](c1ccc(Cl)cc1Cl)N(C(=O)[C@@]([O-])([SiH3])c1cccc(C)c1)C1CC1 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', 'Cl', '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.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, 5, 7, 1, 1, 1, 1, 16, 1, 1, 16, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 13, 6, 13, 4, 6, 6, 10, 10, 6, 7, 10, 10, 10, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 12, 12, 26, 26, 26, 26, 26, 10, 10, 10, 4, 4, 2, 4, 4, 4, 4, 12, 12, 12, 12, 12] 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: 158 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895016 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895016/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895016 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 733) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/733 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/733' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](c1ccc(Cl)cc1Cl)N(C(=O)[C@]([O-])([SiH3])c1cccc(C)c1)C1CC1) `ZINC001521895016.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521895016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521895016 none CCOC(=O)[C@H](c1ccc(Cl)cc1Cl)N(C(=O)[C@]([O-])([SiH3])c1cccc(C)c1)C1CC1 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', 'Cl', '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.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, 5, 7, 1, 1, 1, 1, 16, 1, 1, 16, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 21, 20, 6, 20, 5, 6, 6, 12, 12, 6, 6, 12, 12, 12, 3, 1, 3, 1, 1, 1, 4, 4, 2, 4, 4, 4, 5, 10, 10, 25, 25, 25, 25, 25, 12, 12, 12, 4, 4, 2, 4, 4, 4, 4, 10, 10, 10, 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]) total number of confs: 135 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895016 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521895016 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895016/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895016/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895016 Building ZINC001521895016 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895016' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895016 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521895016 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895016/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895016 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 732) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOC(=O)[C@H](c1ccc(Cl)cc1Cl)N(C(=O)[C@@]([O-])([SiH3])c1cccc(C)c1)C1CC1) `ZINC001521895016.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521895016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521895016 none CCOC(=O)[C@H](c1ccc(Cl)cc1Cl)N(C(=O)[C@@]([O-])([SiH3])c1cccc(C)c1)C1CC1 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', 'Cl', '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.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, 5, 7, 1, 1, 1, 1, 16, 1, 1, 16, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 13, 6, 13, 4, 6, 6, 10, 10, 6, 7, 10, 10, 10, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 12, 12, 26, 26, 26, 26, 26, 10, 10, 10, 4, 4, 2, 4, 4, 4, 4, 12, 12, 12, 12, 12] 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: 158 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895016 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895016/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895016 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 733) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOC(=O)[C@H](c1ccc(Cl)cc1Cl)N(C(=O)[C@]([O-])([SiH3])c1cccc(C)c1)C1CC1) `ZINC001521895016.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521895016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521895016 none CCOC(=O)[C@H](c1ccc(Cl)cc1Cl)N(C(=O)[C@]([O-])([SiH3])c1cccc(C)c1)C1CC1 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', 'Cl', '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.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, 5, 7, 1, 1, 1, 1, 16, 1, 1, 16, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 21, 20, 6, 20, 5, 6, 6, 12, 12, 6, 6, 12, 12, 12, 3, 1, 3, 1, 1, 1, 4, 4, 2, 4, 4, 4, 5, 10, 10, 25, 25, 25, 25, 25, 12, 12, 12, 4, 4, 2, 4, 4, 4, 4, 10, 10, 10, 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]) total number of confs: 135 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895016 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521895016 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895016/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895016/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895016 Building ZINC001521895017 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895017' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895017 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521895017 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895017/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895017 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/734 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](c1ccc(Cl)cc1Cl)N(C(=O)[C@@]([O-])([SiH3])c1cccc(C)c1)C1CC1) `ZINC001521895017.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521895017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521895017 none CCOC(=O)[C@@H](c1ccc(Cl)cc1Cl)N(C(=O)[C@@]([O-])([SiH3])c1cccc(C)c1)C1CC1 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', 'Cl', '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.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, 5, 7, 1, 1, 1, 1, 16, 1, 1, 16, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 27, 9, 27, 6, 9, 9, 14, 14, 9, 9, 14, 14, 14, 4, 1, 4, 1, 1, 1, 4, 4, 2, 4, 4, 4, 6, 8, 8, 29, 29, 29, 29, 29, 14, 14, 14, 4, 4, 2, 4, 4, 4, 4, 8, 8, 8, 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]) total number of confs: 123 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895017 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895017/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895017 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 735) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/735 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/735' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](c1ccc(Cl)cc1Cl)N(C(=O)[C@]([O-])([SiH3])c1cccc(C)c1)C1CC1) `ZINC001521895017.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521895017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895017/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521895017 none CCOC(=O)[C@@H](c1ccc(Cl)cc1Cl)N(C(=O)[C@]([O-])([SiH3])c1cccc(C)c1)C1CC1 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', 'Cl', '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.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, 5, 7, 1, 1, 1, 1, 16, 1, 1, 16, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 7, 14, 4, 7, 7, 10, 10, 7, 8, 10, 10, 10, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 13, 13, 24, 24, 24, 24, 24, 10, 10, 10, 4, 4, 2, 4, 4, 4, 4, 13, 13, 13, 13, 13] 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: 143 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895017 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521895017 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895017/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895017/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895017 Building ZINC001521895017 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895017' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895017 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521895017 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895017/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895017 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 734) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOC(=O)[C@@H](c1ccc(Cl)cc1Cl)N(C(=O)[C@@]([O-])([SiH3])c1cccc(C)c1)C1CC1) `ZINC001521895017.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521895017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521895017 none CCOC(=O)[C@@H](c1ccc(Cl)cc1Cl)N(C(=O)[C@@]([O-])([SiH3])c1cccc(C)c1)C1CC1 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', 'Cl', '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.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, 5, 7, 1, 1, 1, 1, 16, 1, 1, 16, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 27, 9, 27, 6, 9, 9, 14, 14, 9, 9, 14, 14, 14, 4, 1, 4, 1, 1, 1, 4, 4, 2, 4, 4, 4, 6, 8, 8, 29, 29, 29, 29, 29, 14, 14, 14, 4, 4, 2, 4, 4, 4, 4, 8, 8, 8, 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]) total number of confs: 123 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895017 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895017/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895017 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 735) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOC(=O)[C@@H](c1ccc(Cl)cc1Cl)N(C(=O)[C@]([O-])([SiH3])c1cccc(C)c1)C1CC1) `ZINC001521895017.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521895017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895017/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001521895017 none CCOC(=O)[C@@H](c1ccc(Cl)cc1Cl)N(C(=O)[C@]([O-])([SiH3])c1cccc(C)c1)C1CC1 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', 'Cl', '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.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, 5, 7, 1, 1, 1, 1, 16, 1, 1, 16, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 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, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 7, 14, 4, 7, 7, 10, 10, 7, 8, 10, 10, 10, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 13, 13, 24, 24, 24, 24, 24, 10, 10, 10, 4, 4, 2, 4, 4, 4, 4, 13, 13, 13, 13, 13] 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: 143 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895017 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521895017 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895017/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895017/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521895017 Building ZINC001521896157 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521896157' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521896157 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521896157 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521896157/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521896157 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/736 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ncnc3c2c(C)c(C)n3c2ccc(C)cc2)cc1Cl) `ZINC001521896157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521896157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521896157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001521896157 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ncnc3c2c(C)c(C)n3c2ccc(C)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', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 5, 1, 5, 8, 1, 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, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 18, 18, 18, 18, 18, 18, 6, 6, 6, 12, 12, 12, 6, 6, 4, 10, 10, 10, 10, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 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: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521896157 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521896157/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521896157 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 737) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/737 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/737' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ncnc3c2c(C)c(C)n3c2ccc(C)cc2)cc1Cl) `ZINC001521896157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521896157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521896157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001521896157 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ncnc3c2c(C)c(C)n3c2ccc(C)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', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 5, 1, 5, 8, 1, 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, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 6, 6, 6, 12, 12, 12, 6, 6, 4, 10, 10, 10, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 17, 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: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521896157 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521896157 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521896157/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521896157/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521896157 Building ZINC001521896157 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521896157' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521896157 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001521896157 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521896157/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521896157 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 736) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ncnc3c2c(C)c(C)n3c2ccc(C)cc2)cc1Cl) `ZINC001521896157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001521896157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521896157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001521896157 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ncnc3c2c(C)c(C)n3c2ccc(C)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', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 5, 1, 5, 8, 1, 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, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 18, 18, 18, 18, 18, 18, 6, 6, 6, 12, 12, 12, 6, 6, 4, 10, 10, 10, 10, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18, 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: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521896157 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521896157/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521896157 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 737) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ncnc3c2c(C)c(C)n3c2ccc(C)cc2)cc1Cl) `ZINC001521896157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001521896157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521896157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001521896157 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ncnc3c2c(C)c(C)n3c2ccc(C)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', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 1, 5, 1, 5, 8, 1, 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, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens 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, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 6, 6, 6, 12, 12, 12, 6, 6, 4, 10, 10, 10, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 17, 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: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521896157 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001521896157 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521896157/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521896157/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001521896157 Building ZINC001522016918 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522016918' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522016918 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522016918 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522016918/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522016918 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/738 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/738' -> `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(c3ccccc3Br)CCCCC2)cn1) `ZINC001522016918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522016918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522016918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001522016918 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCC2(c3ccccc3Br)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', 'C.ar', 'C.ar', 'Br', '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, 1, 1, 17, 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: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 12, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 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: 114 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522016918 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522016918/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522016918 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 739) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/739 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/739' -> `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(c3ccccc3Br)CCCCC2)cn1) `ZINC001522016918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522016918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522016918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001522016918 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCC2(c3ccccc3Br)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', 'C.ar', 'C.ar', 'Br', '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, 1, 1, 17, 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: [11, 6, 11, 11, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 2, 12, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 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: 114 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522016918 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522016918 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522016918/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522016918/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522016918 Building ZINC001522016918 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522016918' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522016918 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522016918 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522016918/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522016918 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 738) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCC2(c3ccccc3Br)CCCCC2)cn1) `ZINC001522016918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522016918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522016918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001522016918 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCC2(c3ccccc3Br)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', 'C.ar', 'C.ar', 'Br', '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, 1, 1, 17, 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: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 12, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 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: 114 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522016918 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522016918/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522016918 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 739) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCC2(c3ccccc3Br)CCCCC2)cn1) `ZINC001522016918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522016918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522016918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001522016918 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCC2(c3ccccc3Br)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', 'C.ar', 'C.ar', 'Br', '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, 1, 1, 17, 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: [11, 6, 11, 11, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 2, 12, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 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: 114 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522016918 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522016918 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522016918/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522016918/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522016918 Building ZINC001522029904 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029904' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029904 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522029904 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029904/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029904 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/740 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](c2cccc(Br)c2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001522029904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522029904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001522029904 none O=C(N1CC[C@@H](c2cccc(Br)c2)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 14, 14, 14, 14, 14, 50, 50, 48, 50, 50, 50, 14, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 14, 14, 14, 14, 50, 50, 50, 50, 14, 14, 2, 1, 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]) total number of confs: 84 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029904 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029904/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029904 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 741) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/741 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/741' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](c2cccc(Br)c2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001522029904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522029904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001522029904 none O=C(N1CC[C@@H](c2cccc(Br)c2)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 12, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 12, 12, 12, 12, 50, 50, 50, 50, 12, 12, 2, 1, 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]) total number of confs: 73 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029904 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522029904 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029904/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029904/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029904 Building ZINC001522029904 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029904' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029904 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522029904 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029904/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029904 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 740) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(N1CC[C@@H](c2cccc(Br)c2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001522029904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522029904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001522029904 none O=C(N1CC[C@@H](c2cccc(Br)c2)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 14, 14, 14, 14, 14, 50, 50, 48, 50, 50, 50, 14, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 14, 14, 14, 14, 50, 50, 50, 50, 14, 14, 2, 1, 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]) total number of confs: 84 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029904 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029904/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029904 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 741) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(N1CC[C@@H](c2cccc(Br)c2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001522029904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522029904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001522029904 none O=C(N1CC[C@@H](c2cccc(Br)c2)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 12, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 12, 12, 12, 12, 50, 50, 50, 50, 12, 12, 2, 1, 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]) total number of confs: 73 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029904 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522029904 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029904/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029904/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029904 Building ZINC001522029907 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029907' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029907 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522029907 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029907/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029907 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/742 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](c2cccc(Br)c2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001522029907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522029907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001522029907 none O=C(N1CC[C@H](c2cccc(Br)c2)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 14, 14, 14, 14, 14, 50, 50, 37, 50, 50, 50, 14, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 50, 50, 50, 50, 14, 14, 2, 2, 2] 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]) total number of confs: 122 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029907 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029907/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029907 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 743) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/743 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/743' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](c2cccc(Br)c2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001522029907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522029907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001522029907 none O=C(N1CC[C@H](c2cccc(Br)c2)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 12, 12, 12, 12, 12, 49, 49, 36, 49, 49, 49, 12, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 12, 12, 12, 12, 49, 49, 36, 49, 12, 12, 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, 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/12845/xbi-8058088.35/working/building/ZINC001522029907 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522029907 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029907/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029907/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029907 Building ZINC001522029907 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029907' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029907 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522029907 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029907/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029907 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 742) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(N1CC[C@H](c2cccc(Br)c2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001522029907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522029907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001522029907 none O=C(N1CC[C@H](c2cccc(Br)c2)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 14, 14, 14, 14, 14, 50, 50, 37, 50, 50, 50, 14, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 50, 50, 50, 50, 14, 14, 2, 2, 2] 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]) total number of confs: 122 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029907 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029907/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029907 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 743) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(N1CC[C@H](c2cccc(Br)c2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001522029907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522029907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001522029907 none O=C(N1CC[C@H](c2cccc(Br)c2)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', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 12, 12, 12, 12, 12, 49, 49, 36, 49, 49, 49, 12, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 12, 12, 12, 12, 49, 49, 36, 49, 12, 12, 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, 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/12845/xbi-8058088.35/working/building/ZINC001522029907 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522029907 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029907/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029907/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522029907 Building ZINC001522043848 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522043848' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522043848 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522043848 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522043848/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522043848 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/744 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(C)c(F)c1)CCC2) `ZINC001522043848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522043848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522043848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001522043848 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(C)c(F)c1)CCC2 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', '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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 5, 1, 15, 1, 5, 5, 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, 3, 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] 0 hydrogens need rotated 50 conformations 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, 5, 5, 5, 13, 13, 13, 13, 13, 23, 23, 44, 44, 44, 44, 44, 44, 44, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3, 5, 44, 44, 44, 44, 44, 44, 13, 13, 13, 13, 13, 13] 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: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522043848 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522043848/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522043848 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 745) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/745 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/745' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(C)c(F)c1)CCC2) `ZINC001522043848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522043848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522043848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001522043848 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(C)c(F)c1)CCC2 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', '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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 5, 1, 15, 1, 5, 5, 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, 3, 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] 0 hydrogens need rotated 50 conformations 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, 5, 5, 5, 11, 11, 11, 11, 11, 19, 19, 49, 49, 49, 49, 49, 49, 49, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 5, 49, 49, 49, 49, 49, 49, 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522043848 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522043848 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522043848/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522043848/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522043848 Building ZINC001522043848 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522043848' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522043848 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522043848 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522043848/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522043848 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 744) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(C)c(F)c1)CCC2) `ZINC001522043848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522043848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522043848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001522043848 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(C)c(F)c1)CCC2 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', '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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 5, 1, 15, 1, 5, 5, 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, 3, 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] 0 hydrogens need rotated 50 conformations 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, 5, 5, 5, 13, 13, 13, 13, 13, 23, 23, 44, 44, 44, 44, 44, 44, 44, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3, 5, 44, 44, 44, 44, 44, 44, 13, 13, 13, 13, 13, 13] 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: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522043848 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522043848/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522043848 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 745) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(C)c(F)c1)CCC2) `ZINC001522043848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522043848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522043848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001522043848 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1sc2c(c1C(=O)c1ccc(C)c(F)c1)CCC2 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', '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, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 14, 1, 1, 1, 1, 11, 1, 1, 1, 1, 5, 1, 15, 1, 5, 5, 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, 3, 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] 0 hydrogens need rotated 50 conformations 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, 5, 5, 5, 11, 11, 11, 11, 11, 19, 19, 49, 49, 49, 49, 49, 49, 49, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 5, 49, 49, 49, 49, 49, 49, 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522043848 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522043848 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522043848/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522043848/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522043848 Building ZINC001522110457 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522110457' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522110457 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522110457 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522110457/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522110457 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/746 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cn(c2ccccc2)nc1c1ccc(F)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001522110457.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522110457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522110457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001522110457 none O=C(NCc1cn(c2ccccc2)nc1c1ccc(F)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', '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, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 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, 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] 0 hydrogens need rotated 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, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 46, 46, 45, 45, 46, 46, 1, 1, 1, 5, 5, 5, 5, 5, 2, 14, 14, 45, 45, 45, 45, 45, 45, 46, 46, 46, 46, 5, 5] 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522110457 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522110457/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522110457 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 747) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/747 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/747' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cn(c2ccccc2)nc1c1ccc(F)cc1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001522110457.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522110457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522110457/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001522110457 none O=C(NCc1cn(c2ccccc2)nc1c1ccc(F)cc1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', '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, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 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, 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] 0 hydrogens need rotated 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, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 46, 46, 45, 45, 46, 46, 1, 1, 1, 5, 5, 5, 5, 5, 2, 14, 14, 45, 45, 45, 45, 45, 45, 46, 46, 46, 46, 5, 5] 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522110457 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522110457 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522110457/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522110457/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522110457 Building ZINC001522110457 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522110457' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522110457 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522110457 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522110457/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522110457 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 746) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/746: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cn(c2ccccc2)nc1c1ccc(F)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001522110457.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522110457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522110457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001522110457 none O=C(NCc1cn(c2ccccc2)nc1c1ccc(F)cc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', '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, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 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, 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] 0 hydrogens need rotated 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, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 46, 46, 45, 45, 46, 46, 1, 1, 1, 5, 5, 5, 5, 5, 2, 14, 14, 45, 45, 45, 45, 45, 45, 46, 46, 46, 46, 5, 5] 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522110457 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522110457/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522110457 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 747) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/747: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cn(c2ccccc2)nc1c1ccc(F)cc1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001522110457.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522110457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522110457/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001522110457 none O=C(NCc1cn(c2ccccc2)nc1c1ccc(F)cc1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.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', '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, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 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, 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] 0 hydrogens need rotated 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, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 46, 46, 45, 45, 46, 46, 1, 1, 1, 5, 5, 5, 5, 5, 2, 14, 14, 45, 45, 45, 45, 45, 45, 46, 46, 46, 46, 5, 5] 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522110457 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522110457 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522110457/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522110457/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522110457 Building ZINC001522245251 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522245251' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522245251 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522245251 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522245251/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522245251 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/748 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/748' -> `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])c2ccc(Cl)cc2)c1C) `ZINC001522245251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522245251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522245251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001522245251 none Cc1nn(c2ccc(Br)cc2)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)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', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', '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, 16, 1, 1, 1, 5, 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] 0 hydrogens 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, 41, 41, 41, 49, 49, 41, 41, 49, 49, 11, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 41, 41, 41, 41, 41, 49, 49, 49, 49, 11, 5, 5, 5, 5, 41, 41, 41] 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: 117 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522245251 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522245251/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522245251 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 749) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/749 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/749' -> `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])c2ccc(Cl)cc2)c1C) `ZINC001522245251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522245251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522245251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001522245251 none Cc1nn(c2ccc(Br)cc2)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)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', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', '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, 16, 1, 1, 1, 5, 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] 0 hydrogens 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, 41, 41, 41, 49, 49, 46, 47, 49, 49, 11, 6, 1, 6, 1, 1, 1, 5, 5, 1, 5, 5, 5, 41, 41, 41, 41, 41, 49, 49, 49, 49, 11, 5, 5, 5, 5, 41, 41, 41] 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]) total number of confs: 111 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522245251 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522245251 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522245251/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522245251/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522245251 Building ZINC001522245251 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522245251' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522245251 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522245251 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522245251/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522245251 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 748) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccc(Br)cc2)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c1C) `ZINC001522245251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522245251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522245251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001522245251 none Cc1nn(c2ccc(Br)cc2)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)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', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', '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, 16, 1, 1, 1, 5, 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] 0 hydrogens 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, 41, 41, 41, 49, 49, 41, 41, 49, 49, 11, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 41, 41, 41, 41, 41, 49, 49, 49, 49, 11, 5, 5, 5, 5, 41, 41, 41] 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: 117 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522245251 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522245251/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522245251 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 749) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccc(Br)cc2)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c1C) `ZINC001522245251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522245251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522245251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001522245251 none Cc1nn(c2ccc(Br)cc2)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)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', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', '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, 16, 1, 1, 1, 5, 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] 0 hydrogens 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, 41, 41, 41, 49, 49, 46, 47, 49, 49, 11, 6, 1, 6, 1, 1, 1, 5, 5, 1, 5, 5, 5, 41, 41, 41, 41, 41, 49, 49, 49, 49, 11, 5, 5, 5, 5, 41, 41, 41] 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]) total number of confs: 111 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522245251 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522245251 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522245251/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522245251/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522245251 Building ZINC001522305485 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305485' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305485 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522305485 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305485/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305485 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/750 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)n1c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2nc1C(F)(F)F) `ZINC001522305485.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522305485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001522305485 none CC[C@@H](C)n1c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2nc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', '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', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 14, 14, 14, 8, 13, 13, 13, 13, 13, 13, 13, 13, 19, 19, 19, 19, 19, 13, 13, 13, 13, 13, 3, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 13] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305485 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305485/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305485 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 751) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/751 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/751' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)n1c2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2nc1C(F)(F)F) `ZINC001522305485.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522305485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305485/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001522305485 none CC[C@@H](C)n1c2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2nc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', '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', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 14, 14, 14, 7, 12, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 12, 12, 12, 12, 12, 2, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 12] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305485 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522305485 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305485/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305485/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305485 Building ZINC001522305485 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305485' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305485 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522305485 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305485/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305485 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 750) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/750: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)n1c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2nc1C(F)(F)F) `ZINC001522305485.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522305485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001522305485 none CC[C@@H](C)n1c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2nc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', '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', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 14, 14, 14, 8, 13, 13, 13, 13, 13, 13, 13, 13, 19, 19, 19, 19, 19, 13, 13, 13, 13, 13, 3, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 13] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305485 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305485/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305485 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 751) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/751: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)n1c2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2nc1C(F)(F)F) `ZINC001522305485.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522305485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305485/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001522305485 none CC[C@@H](C)n1c2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2nc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', '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', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 14, 14, 14, 7, 12, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 12, 12, 12, 12, 12, 2, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 12] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305485 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522305485 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305485/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305485/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305485 Building ZINC001522305488 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305488' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305488 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522305488 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305488/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305488 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/752 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)n1c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2nc1C(F)(F)F) `ZINC001522305488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522305488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001522305488 none CC[C@H](C)n1c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2nc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', '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', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 12] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305488 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305488/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305488 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 753) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/753 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/753' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)n1c2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2nc1C(F)(F)F) `ZINC001522305488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522305488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001522305488 none CC[C@H](C)n1c2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2nc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', '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', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 12, 12, 12, 7, 12, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 12, 12, 12, 12, 12, 2, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 12] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305488 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522305488 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305488/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305488/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305488 Building ZINC001522305488 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305488' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305488 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522305488 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305488/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305488 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 752) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC[C@H](C)n1c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2nc1C(F)(F)F) `ZINC001522305488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522305488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001522305488 none CC[C@H](C)n1c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2nc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', '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', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 12] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305488 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305488/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305488 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 753) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC[C@H](C)n1c2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2nc1C(F)(F)F) `ZINC001522305488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522305488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001522305488 none CC[C@H](C)n1c2ccc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)cc2nc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', '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', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 12, 12, 12, 7, 12, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 12, 12, 12, 12, 12, 2, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 12] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305488 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522305488 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305488/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305488/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522305488 Building ZINC001522311240 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522311240' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522311240 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522311240 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522311240/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522311240 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/754 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1Cl) `ZINC001522311240.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522311240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522311240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001522311240 none CCCCOc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1Cl 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 20, 11, 11, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 31, 31, 11, 11, 4, 4, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 11] 50 rigid atoms, others: [45, 27, 9, 10, 11, 44, 13, 12, 15, 16, 17, 18, 19, 20, 14, 54, 55, 46, 26, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50, 51, 52, 56]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522311240 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522311240/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522311240 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 755) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/755 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/755' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOc1ccc(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1Cl) `ZINC001522311240.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522311240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522311240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001522311240 none CCCCOc1ccc(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1Cl 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 19, 11, 11, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 29, 29, 11, 11, 4, 4, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 11] 50 rigid atoms, others: [45, 27, 9, 10, 11, 44, 13, 12, 15, 16, 17, 18, 19, 20, 14, 54, 55, 46, 26, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50, 51, 52, 56]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522311240 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522311240 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522311240/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522311240/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522311240 Building ZINC001522311240 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522311240' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522311240 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522311240 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522311240/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522311240 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 754) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCCCOc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1Cl) `ZINC001522311240.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522311240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522311240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001522311240 none CCCCOc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1Cl 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 20, 11, 11, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 31, 31, 11, 11, 4, 4, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 11] 50 rigid atoms, others: [45, 27, 9, 10, 11, 44, 13, 12, 15, 16, 17, 18, 19, 20, 14, 54, 55, 46, 26, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50, 51, 52, 56]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522311240 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522311240/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522311240 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 755) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCCCOc1ccc(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1Cl) `ZINC001522311240.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522311240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522311240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001522311240 none CCCCOc1ccc(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1Cl 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 19, 11, 11, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 29, 29, 11, 11, 4, 4, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 11] 50 rigid atoms, others: [45, 27, 9, 10, 11, 44, 13, 12, 15, 16, 17, 18, 19, 20, 14, 54, 55, 46, 26, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 48, 49, 50, 51, 52, 56]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522311240 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522311240 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522311240/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522311240/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522311240 Building ZINC001522429782 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429782' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429782 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522429782 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429782/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429782 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/756 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/756' -> `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)cc2)[C@@H](CC)CN1C(=O)OCc1ccccc1) `ZINC001522429782.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522429782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001522429782 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)[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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 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, 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, 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: [5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 5, 10, 10, 14, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50] 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429782 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429782/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429782 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 757) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/757 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/757' -> `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)cc2)[C@@H](CC)CN1C(=O)OCc1ccccc1) `ZINC001522429782.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522429782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001522429782 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)[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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 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, 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, 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: [3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 3, 3, 5, 3, 3, 3, 7, 7, 11, 38, 50, 50, 38, 50, 50, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 5, 5, 5, 5, 5, 3, 3, 38, 38, 50, 50, 38, 50, 50] 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 207 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429782 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522429782 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429782/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429782/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429782 Building ZINC001522429782 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429782' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429782 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522429782 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429782/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429782 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 756) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)[C@@H](CC)CN1C(=O)OCc1ccccc1) `ZINC001522429782.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522429782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001522429782 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)[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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 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, 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, 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: [5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 5, 10, 10, 14, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 50, 50, 50, 50, 50, 50, 50] 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429782 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429782/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429782 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 757) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)[C@@H](CC)CN1C(=O)OCc1ccccc1) `ZINC001522429782.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522429782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001522429782 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)[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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 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, 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, 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: [3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 3, 3, 5, 3, 3, 3, 7, 7, 11, 38, 50, 50, 38, 50, 50, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 5, 5, 5, 5, 5, 3, 3, 38, 38, 50, 50, 38, 50, 50] 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 207 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429782 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522429782 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429782/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429782/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429782 Building ZINC001522429783 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429783' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429783 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522429783 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429783/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429783 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/758 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/758' -> `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)cc2)[C@H](CC)CN1C(=O)OCc1ccccc1) `ZINC001522429783.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522429783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001522429783 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)[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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 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, 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, 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: [4, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 3, 3, 3, 5, 5, 9, 34, 42, 42, 34, 42, 42, 4, 4, 4, 4, 4, 3, 3, 1, 1, 1, 1, 4, 4, 4, 4, 4, 3, 3, 34, 34, 42, 42, 34, 42, 42] 50 rigid atoms, others: [43, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 169 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429783 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429783/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429783 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 759) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/759 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/759' -> `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)cc2)[C@H](CC)CN1C(=O)OCc1ccccc1) `ZINC001522429783.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522429783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429783/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001522429783 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)[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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 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, 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, 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: [4, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 2, 2, 2, 5, 2, 2, 2, 4, 4, 8, 37, 44, 44, 37, 44, 44, 4, 4, 4, 4, 4, 2, 2, 3, 3, 3, 3, 5, 5, 5, 5, 5, 2, 2, 37, 37, 44, 44, 37, 44, 44] 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 193 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429783 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522429783 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429783/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429783/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429783 Building ZINC001522429783 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429783' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429783 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522429783 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429783/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429783 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 758) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)[C@H](CC)CN1C(=O)OCc1ccccc1) `ZINC001522429783.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522429783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001522429783 none CC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)[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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 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, 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, 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: [4, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 3, 3, 3, 5, 5, 9, 34, 42, 42, 34, 42, 42, 4, 4, 4, 4, 4, 3, 3, 1, 1, 1, 1, 4, 4, 4, 4, 4, 3, 3, 34, 34, 42, 42, 34, 42, 42] 50 rigid atoms, others: [43, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 169 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429783 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429783/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429783 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 759) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)[C@H](CC)CN1C(=O)OCc1ccccc1) `ZINC001522429783.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522429783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429783/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001522429783 none CC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)[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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 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, 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, 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: [4, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 2, 2, 2, 5, 2, 2, 2, 4, 4, 8, 37, 44, 44, 37, 44, 44, 4, 4, 4, 4, 4, 2, 2, 3, 3, 3, 3, 5, 5, 5, 5, 5, 2, 2, 37, 37, 44, 44, 37, 44, 44] 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 193 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429783 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522429783 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429783/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429783/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429783 Building ZINC001522429784 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429784' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429784 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522429784 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429784/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429784 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/760 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/760' -> `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)cc1) `ZINC001522429784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522429784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001522429784 none CC[C@@H]1CN(C(=O)OCc2ccccc2)[C@@H](CC)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 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, 7, 7, 7] 0 hydrogens 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, 5, 5, 10, 10, 14, 39, 50, 50, 39, 50, 50, 5, 5, 5, 6, 5, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 5, 5, 5, 5, 5, 5, 39, 39, 50, 50, 39, 50, 50, 6, 6, 6, 6, 6, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [22, 24, 25, 26] 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, 55, 56, 57]) total number of confs: 196 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429784 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429784/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429784 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 761) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/761 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/761' -> `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)cc1) `ZINC001522429784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522429784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001522429784 none CC[C@@H]1CN(C(=O)OCc2ccccc2)[C@@H](CC)CN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 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, 7, 7, 7] 0 hydrogens 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, 5, 5, 10, 10, 14, 38, 50, 50, 38, 50, 50, 5, 5, 5, 6, 5, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 5, 5, 5, 5, 5, 5, 38, 38, 50, 50, 38, 50, 50, 6, 6, 6, 6, 6, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [22, 24, 25, 26] 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, 55, 56, 57]) total number of confs: 201 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429784 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522429784 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429784/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429784/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429784 Building ZINC001522429784 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429784' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429784 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522429784 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429784/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429784 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 760) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC[C@@H]1CN(C(=O)OCc2ccccc2)[C@@H](CC)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001522429784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522429784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001522429784 none CC[C@@H]1CN(C(=O)OCc2ccccc2)[C@@H](CC)CN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 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, 7, 7, 7] 0 hydrogens 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, 5, 5, 10, 10, 14, 39, 50, 50, 39, 50, 50, 5, 5, 5, 6, 5, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 5, 5, 5, 5, 5, 5, 39, 39, 50, 50, 39, 50, 50, 6, 6, 6, 6, 6, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [22, 24, 25, 26] 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, 55, 56, 57]) total number of confs: 196 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429784 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429784/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429784 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 761) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC[C@@H]1CN(C(=O)OCc2ccccc2)[C@@H](CC)CN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001522429784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522429784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001522429784 none CC[C@@H]1CN(C(=O)OCc2ccccc2)[C@@H](CC)CN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 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, 7, 7, 7] 0 hydrogens 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, 5, 5, 10, 10, 14, 38, 50, 50, 38, 50, 50, 5, 5, 5, 6, 5, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 5, 5, 5, 5, 5, 5, 38, 38, 50, 50, 38, 50, 50, 6, 6, 6, 6, 6, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [22, 24, 25, 26] 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, 55, 56, 57]) total number of confs: 201 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429784 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522429784 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429784/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429784/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429784 Building ZINC001522429785 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429785' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429785 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522429785 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429785/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429785 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/762 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/762' -> `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)cc2)[C@@H](CC)CN1C(=O)OCc1ccccc1) `ZINC001522429785.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522429785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001522429785 none CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)[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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 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, 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, 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: [5, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 3, 3, 5, 3, 3, 3, 5, 5, 9, 39, 45, 45, 40, 45, 45, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 39, 39, 45, 45, 45, 45, 45] 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 196 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429785 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429785/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429785 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 763) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/763 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/763' -> `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)cc2)[C@@H](CC)CN1C(=O)OCc1ccccc1) `ZINC001522429785.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522429785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429785/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001522429785 none CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)[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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 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, 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, 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: [4, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 3, 3, 3, 6, 6, 10, 36, 44, 44, 38, 44, 44, 4, 4, 4, 4, 4, 3, 3, 1, 1, 1, 1, 4, 4, 4, 4, 4, 3, 3, 36, 36, 44, 44, 44, 44, 44] 50 rigid atoms, others: [43, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 185 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429785 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522429785 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429785/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429785/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429785 Building ZINC001522429785 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429785' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429785 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522429785 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429785/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429785 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 762) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)[C@@H](CC)CN1C(=O)OCc1ccccc1) `ZINC001522429785.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522429785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001522429785 none CC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)[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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 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, 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, 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: [5, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 3, 3, 5, 3, 3, 3, 5, 5, 9, 39, 45, 45, 40, 45, 45, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 39, 39, 45, 45, 45, 45, 45] 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, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 196 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429785 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429785/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429785 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 763) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)[C@@H](CC)CN1C(=O)OCc1ccccc1) `ZINC001522429785.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522429785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429785/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001522429785 none CC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)[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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 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, 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, 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: [4, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 3, 3, 3, 6, 6, 10, 36, 44, 44, 38, 44, 44, 4, 4, 4, 4, 4, 3, 3, 1, 1, 1, 1, 4, 4, 4, 4, 4, 3, 3, 36, 36, 44, 44, 44, 44, 44] 50 rigid atoms, others: [43, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 185 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429785 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522429785 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429785/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429785/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522429785 Building ZINC001522436440 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522436440' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522436440 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522436440 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522436440/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522436440 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/764 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/764' -> `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)c1ccc(OCc2ccccc2)cc1) `ZINC001522436440.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522436440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522436440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001522436440 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)c1ccc(OCc2ccccc2)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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 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] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 10, 10, 5, 5, 19, 19, 37, 37, 19, 37, 37, 10, 10, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 5, 5, 5, 10, 10, 19, 19, 37, 37, 19, 37, 37, 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]) total number of confs: 158 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522436440 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522436440/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522436440 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 765) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/765 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/765' -> `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)c1ccc(OCc2ccccc2)cc1) `ZINC001522436440.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522436440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522436440/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001522436440 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)c1ccc(OCc2ccccc2)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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 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] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 11, 11, 8, 11, 20, 20, 35, 35, 20, 35, 35, 11, 11, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 5, 5, 5, 11, 11, 20, 20, 35, 35, 20, 35, 35, 11, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 148 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522436440 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522436440 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522436440/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522436440/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522436440 Building ZINC001522436440 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522436440' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522436440 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522436440 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522436440/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522436440 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 764) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)c1ccc(OCc2ccccc2)cc1) `ZINC001522436440.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522436440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522436440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001522436440 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)c1ccc(OCc2ccccc2)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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 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] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 10, 10, 5, 5, 19, 19, 37, 37, 19, 37, 37, 10, 10, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 5, 5, 5, 10, 10, 19, 19, 37, 37, 19, 37, 37, 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]) total number of confs: 158 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522436440 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522436440/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522436440 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 765) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)c1ccc(OCc2ccccc2)cc1) `ZINC001522436440.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522436440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522436440/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001522436440 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)c1ccc(OCc2ccccc2)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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 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] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 11, 11, 8, 11, 20, 20, 35, 35, 20, 35, 35, 11, 11, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 5, 5, 5, 11, 11, 20, 20, 35, 35, 20, 35, 35, 11, 11] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 148 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522436440 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522436440 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522436440/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522436440/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522436440 Building ZINC001522478024 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478024' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478024 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522478024 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478024/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478024 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/766 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCCSc1ccccc1Br)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001522478024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522478024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001522478024 none O=C(NCCCCSc1ccccc1Br)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', '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'] 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, 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] 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 11, 25, 31, 30, 31, 31, 31, 31, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 10, 10, 11, 10, 11, 11, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 4, 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, 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/12845/xbi-8058088.35/working/building/ZINC001522478024 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478024/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478024 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 767) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/767 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/767' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCCSc1ccccc1Br)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001522478024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522478024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001522478024 none O=C(NCCCCSc1ccccc1Br)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', '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'] 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, 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] 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 12, 12, 26, 32, 32, 32, 32, 32, 32, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 8, 8, 11, 11, 12, 11, 12, 12, 32, 32, 32, 32, 4, 4, 4, 4, 4, 4, 4, 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, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478024 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522478024 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478024/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478024/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478024 Building ZINC001522478024 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478024' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478024 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522478024 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478024/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478024 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 766) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(NCCCCSc1ccccc1Br)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001522478024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522478024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001522478024 none O=C(NCCCCSc1ccccc1Br)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', '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'] 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, 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] 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 11, 25, 31, 30, 31, 31, 31, 31, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 7, 7, 10, 10, 11, 10, 11, 11, 31, 31, 31, 31, 4, 4, 4, 4, 4, 4, 4, 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, 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/12845/xbi-8058088.35/working/building/ZINC001522478024 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478024/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478024 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 767) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(NCCCCSc1ccccc1Br)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001522478024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522478024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001522478024 none O=C(NCCCCSc1ccccc1Br)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 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', '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'] 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, 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] 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 12, 12, 26, 32, 32, 32, 32, 32, 32, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 8, 8, 11, 11, 12, 11, 12, 12, 32, 32, 32, 32, 4, 4, 4, 4, 4, 4, 4, 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, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478024 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522478024 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478024/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478024/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478024 Building ZINC001522478358 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478358' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478358 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522478358 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478358/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478358 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/768 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/768' -> `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(F)c2F)CCCC1) `ZINC001522478358.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522478358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001522478358 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(c2cccc(F)c2F)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', '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, 5, 5, 1, 1, 1, 1, 1, 15, 1, 15, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 20, 37, 40, 40, 40, 40, 40, 40, 40, 37, 37, 37, 37, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 3, 12, 12, 40, 40, 40, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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: 136 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478358 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478358/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478358 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 769) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/769 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/769' -> `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(F)c2F)CCCC1) `ZINC001522478358.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522478358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001522478358 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(c2cccc(F)c2F)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', '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, 5, 5, 1, 1, 1, 1, 1, 15, 1, 15, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 3, 3, 3, 19, 37, 38, 38, 38, 38, 38, 38, 38, 37, 37, 37, 37, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 3, 12, 12, 38, 38, 38, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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: 124 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478358 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522478358 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478358/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478358/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478358 Building ZINC001522478358 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478358' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478358 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522478358 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478358/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478358 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 768) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(c2cccc(F)c2F)CCCC1) `ZINC001522478358.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522478358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001522478358 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(c2cccc(F)c2F)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', '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, 5, 5, 1, 1, 1, 1, 1, 15, 1, 15, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 20, 37, 40, 40, 40, 40, 40, 40, 40, 37, 37, 37, 37, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 3, 12, 12, 40, 40, 40, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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: 136 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478358 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478358/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478358 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 769) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(c2cccc(F)c2F)CCCC1) `ZINC001522478358.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522478358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001522478358 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(c2cccc(F)c2F)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', '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, 5, 5, 1, 1, 1, 1, 1, 15, 1, 15, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 3, 3, 3, 19, 37, 38, 38, 38, 38, 38, 38, 38, 37, 37, 37, 37, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 3, 12, 12, 38, 38, 38, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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: 124 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478358 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522478358 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478358/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478358/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522478358 Building ZINC001522514722 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522514722' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522514722 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522514722 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522514722/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522514722 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/770 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc(NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)c(OCC)cc1NC(=O)c1ccccc1) `ZINC001522514722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522514722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522514722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001522514722 none CCOc1cc(NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)c(OCC)cc1NC(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 12, 5, 5, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 4, 4, 5, 5, 10, 14, 5, 5, 5, 9, 9, 9, 14, 14, 9, 14, 14, 12, 12, 12, 12, 12, 5, 2, 4, 4, 2, 4, 4, 4, 4, 14, 14, 14, 14, 14, 5, 9, 14, 14, 14, 14, 14] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522514722 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522514722/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522514722 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 771) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/771 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/771' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc(NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)c(OCC)cc1NC(=O)c1ccccc1) `ZINC001522514722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522514722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522514722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001522514722 none CCOc1cc(NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)c(OCC)cc1NC(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 12, 5, 5, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 5, 5, 10, 13, 5, 5, 5, 9, 9, 9, 14, 14, 9, 14, 14, 11, 11, 11, 11, 11, 5, 2, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 5, 9, 14, 14, 14, 14, 14] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 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/12845/xbi-8058088.35/working/building/ZINC001522514722 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522514722 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522514722/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522514722/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522514722 Building ZINC001522514722 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522514722' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522514722 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522514722 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522514722/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522514722 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 770) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOc1cc(NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)c(OCC)cc1NC(=O)c1ccccc1) `ZINC001522514722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522514722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522514722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001522514722 none CCOc1cc(NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)c(OCC)cc1NC(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 12, 5, 5, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 4, 4, 5, 5, 10, 14, 5, 5, 5, 9, 9, 9, 14, 14, 9, 14, 14, 12, 12, 12, 12, 12, 5, 2, 4, 4, 2, 4, 4, 4, 4, 14, 14, 14, 14, 14, 5, 9, 14, 14, 14, 14, 14] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522514722 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522514722/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522514722 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 771) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOc1cc(NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)c(OCC)cc1NC(=O)c1ccccc1) `ZINC001522514722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522514722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522514722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001522514722 none CCOc1cc(NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)c(OCC)cc1NC(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 12, 5, 5, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 5, 5, 10, 13, 5, 5, 5, 9, 9, 9, 14, 14, 9, 14, 14, 11, 11, 11, 11, 11, 5, 2, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 5, 9, 14, 14, 14, 14, 14] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 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/12845/xbi-8058088.35/working/building/ZINC001522514722 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522514722 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522514722/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522514722/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522514722 Building ZINC001522526886 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522526886' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522526886 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522526886 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522526886/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522526886 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/772 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(I)ccc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001522526886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522526886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522526886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 34 natoms 33 natoms 32 natoms 31 names: ZINC001522526886 none Cc1cc(I)ccc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'I', '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'] dock atom type numbers: [5, 1, 1, 1, 18, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 9, 10, 36, 36, 9, 9, 1, 9, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 36, 36, 36, 36, 36, 36, 9, 6, 1, 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]) total number of confs: 115 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522526886 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522526886/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522526886 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 773) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/773 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/773' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(I)ccc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001522526886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522526886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522526886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 34 natoms 33 natoms 32 natoms 31 names: ZINC001522526886 none Cc1cc(I)ccc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'I', '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'] dock atom type numbers: [5, 1, 1, 1, 18, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 17, 36, 36, 36, 9, 9, 1, 9, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 36, 36, 36, 36, 36, 36, 9, 6, 1, 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]) total number of confs: 133 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522526886 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522526886 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522526886/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522526886/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522526886 Building ZINC001522526886 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522526886' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522526886 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522526886 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522526886/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522526886 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 772) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1cc(I)ccc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001522526886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522526886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522526886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 34 natoms 33 natoms 32 natoms 31 names: ZINC001522526886 none Cc1cc(I)ccc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'I', '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'] dock atom type numbers: [5, 1, 1, 1, 18, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 9, 10, 36, 36, 9, 9, 1, 9, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 36, 36, 36, 36, 36, 36, 9, 6, 1, 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]) total number of confs: 115 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522526886 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522526886/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522526886 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 773) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1cc(I)ccc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001522526886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522526886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522526886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 34 natoms 33 natoms 32 natoms 31 names: ZINC001522526886 none Cc1cc(I)ccc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'I', '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'] dock atom type numbers: [5, 1, 1, 1, 18, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 17, 36, 36, 36, 9, 9, 1, 9, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 36, 36, 36, 36, 36, 36, 9, 6, 1, 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]) total number of confs: 133 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522526886 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522526886 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522526886/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522526886/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522526886 Building ZINC001522562117 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522562117' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522562117 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522562117 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522562117/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522562117 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/774 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/774' -> `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)cc2)n1) `ZINC001522562117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522562117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522562117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001522562117 none Cc1cc(C)n2c(nnc2c2c(Cl)cccc2NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 46, 46, 46, 46, 46, 25, 25, 25, 25, 25, 25, 25, 8, 8, 1, 8, 1, 1, 1, 6, 6, 1, 1, 6, 6, 46, 46, 46, 46, 46, 46, 46, 46, 25, 25, 25, 8, 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522562117 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522562117/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522562117 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 775) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/775 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/775' -> `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)cc2)n1) `ZINC001522562117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522562117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522562117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001522562117 none Cc1cc(C)n2c(nnc2c2c(Cl)cccc2NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 46, 46, 46, 46, 46, 25, 25, 25, 25, 25, 25, 25, 8, 8, 1, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 46, 46, 46, 46, 46, 46, 46, 46, 25, 25, 25, 8, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522562117 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522562117 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522562117/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522562117/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522562117 Building ZINC001522562117 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522562117' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522562117 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522562117 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522562117/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522562117 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 774) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1cc(C)n2c(nnc2c2c(Cl)cccc2NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n1) `ZINC001522562117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522562117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522562117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001522562117 none Cc1cc(C)n2c(nnc2c2c(Cl)cccc2NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 46, 46, 46, 46, 46, 25, 25, 25, 25, 25, 25, 25, 8, 8, 1, 8, 1, 1, 1, 6, 6, 1, 1, 6, 6, 46, 46, 46, 46, 46, 46, 46, 46, 25, 25, 25, 8, 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522562117 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522562117/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522562117 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 775) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1cc(C)n2c(nnc2c2c(Cl)cccc2NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)n1) `ZINC001522562117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522562117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522562117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001522562117 none Cc1cc(C)n2c(nnc2c2c(Cl)cccc2NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 46, 46, 46, 46, 46, 25, 25, 25, 25, 25, 25, 25, 8, 8, 1, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 46, 46, 46, 46, 46, 46, 46, 46, 25, 25, 25, 8, 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]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522562117 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522562117 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522562117/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522562117/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522562117 Building ZINC001522573846 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522573846' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522573846 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522573846 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522573846/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522573846 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/776 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/776' -> `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(Br)cc1Cl) `ZINC001522573846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522573846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522573846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001522573846 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Br)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.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'] 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, 16, 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, 14, 14, 4, 14, 14, 4, 4, 1, 1, 1, 1, 8, 8, 8, 32, 32, 32, 32, 32, 32, 32, 4, 4, 4, 14, 14, 4, 14, 14, 4, 4, 4, 8, 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]) total number of confs: 83 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522573846 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522573846/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522573846 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 777) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/777 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/777' -> `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(Br)cc1Cl) `ZINC001522573846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522573846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522573846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001522573846 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Br)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.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'] 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, 16, 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, 15, 15, 5, 15, 15, 5, 5, 1, 1, 1, 1, 7, 7, 7, 31, 31, 20, 31, 31, 31, 31, 5, 5, 5, 15, 15, 6, 15, 15, 5, 5, 5, 7, 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: 124 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522573846 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522573846 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522573846/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522573846/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522573846 Building ZINC001522573846 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522573846' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522573846 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522573846 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522573846/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522573846 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 776) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Br)cc1Cl) `ZINC001522573846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522573846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522573846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001522573846 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Br)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.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'] 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, 16, 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, 14, 14, 4, 14, 14, 4, 4, 1, 1, 1, 1, 8, 8, 8, 32, 32, 32, 32, 32, 32, 32, 4, 4, 4, 14, 14, 4, 14, 14, 4, 4, 4, 8, 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]) total number of confs: 83 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522573846 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522573846/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522573846 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 777) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Br)cc1Cl) `ZINC001522573846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522573846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522573846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001522573846 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Br)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.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'] 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, 16, 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, 15, 15, 5, 15, 15, 5, 5, 1, 1, 1, 1, 7, 7, 7, 31, 31, 20, 31, 31, 31, 31, 5, 5, 5, 15, 15, 6, 15, 15, 5, 5, 5, 7, 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: 124 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522573846 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522573846 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522573846/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522573846/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522573846 Building ZINC001522606927 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522606927' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522606927 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522606927 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522606927/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522606927 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/778 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Sc3ccc(Br)cc3)cc2)cn1) `ZINC001522606927.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522606927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522606927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001522606927 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Sc3ccc(Br)cc3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 16, 21, 21, 21, 21, 21, 21, 4, 4, 4, 4, 7, 7, 7, 7, 7, 4, 2, 4, 4, 21, 21, 21, 21, 4, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522606927 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522606927/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522606927 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 779) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/779 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/779' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(Sc3ccc(Br)cc3)cc2)cn1) `ZINC001522606927.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522606927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522606927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001522606927 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(Sc3ccc(Br)cc3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 17, 22, 22, 22, 22, 22, 22, 4, 4, 5, 5, 9, 9, 9, 9, 9, 5, 2, 4, 4, 22, 22, 22, 22, 4, 4, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522606927 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522606927 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522606927/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522606927/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522606927 Building ZINC001522606927 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522606927' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522606927 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522606927 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522606927/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522606927 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 778) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Sc3ccc(Br)cc3)cc2)cn1) `ZINC001522606927.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522606927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522606927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001522606927 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Sc3ccc(Br)cc3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 16, 21, 21, 21, 21, 21, 21, 4, 4, 4, 4, 7, 7, 7, 7, 7, 4, 2, 4, 4, 21, 21, 21, 21, 4, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522606927 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522606927/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522606927 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 779) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(Sc3ccc(Br)cc3)cc2)cn1) `ZINC001522606927.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522606927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522606927/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001522606927 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(Sc3ccc(Br)cc3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 17, 22, 22, 22, 22, 22, 22, 4, 4, 5, 5, 9, 9, 9, 9, 9, 5, 2, 4, 4, 22, 22, 22, 22, 4, 4, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522606927 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522606927 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522606927/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522606927/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522606927 Building ZINC001522682084 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522682084' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522682084 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522682084 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522682084/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522682084 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/780 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2cccc(Br)c2)nc1) `ZINC001522682084.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522682084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522682084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001522682084 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2cccc(Br)c2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', '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, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 17, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 29, 50, 50, 46, 50, 50, 50, 12, 12, 2, 2, 2, 2, 2, 2, 3, 12, 12, 50, 50, 50, 50, 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522682084 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522682084/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522682084 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 781) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/781 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/781' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2cccc(Br)c2)nc1) `ZINC001522682084.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522682084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522682084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001522682084 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2cccc(Br)c2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', '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, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 17, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 28, 50, 50, 50, 50, 50, 50, 12, 12, 2, 2, 2, 2, 2, 2, 3, 12, 12, 50, 50, 50, 50, 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522682084 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522682084 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522682084/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522682084/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522682084 Building ZINC001522682084 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522682084' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522682084 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522682084 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522682084/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522682084 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 780) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2cccc(Br)c2)nc1) `ZINC001522682084.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522682084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522682084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001522682084 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Oc2cccc(Br)c2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', '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, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 17, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 29, 50, 50, 46, 50, 50, 50, 12, 12, 2, 2, 2, 2, 2, 2, 3, 12, 12, 50, 50, 50, 50, 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]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522682084 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522682084/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522682084 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 781) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2cccc(Br)c2)nc1) `ZINC001522682084.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522682084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522682084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001522682084 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc(Oc2cccc(Br)c2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', '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, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 17, 1, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 28, 50, 50, 50, 50, 50, 50, 12, 12, 2, 2, 2, 2, 2, 2, 3, 12, 12, 50, 50, 50, 50, 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522682084 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522682084 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522682084/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522682084/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522682084 Building ZINC001522975805 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522975805' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522975805 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522975805 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522975805/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522975805 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/782 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(F)(F)F)c(Br)c2)cc1Cl) `ZINC001522975805.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522975805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522975805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001522975805 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(F)(F)F)c(Br)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'Br', '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, 1, 5, 15, 15, 15, 1, 17, 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: [13, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 15, 11, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 13, 13, 13, 6, 6, 3, 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522975805 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522975805/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522975805 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 783) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/783 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/783' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(F)(F)F)c(Br)c2)cc1Cl) `ZINC001522975805.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522975805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522975805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001522975805 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(F)(F)F)c(Br)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'Br', '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, 1, 5, 15, 15, 15, 1, 17, 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: [15, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 15, 9, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 15, 15, 15, 6, 6, 3, 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522975805 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522975805 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522975805/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522975805/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522975805 Building ZINC001522975805 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522975805' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522975805 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001522975805 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522975805/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522975805 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 782) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(F)(F)F)c(Br)c2)cc1Cl) `ZINC001522975805.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001522975805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522975805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001522975805 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(F)(F)F)c(Br)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'Br', '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, 1, 5, 15, 15, 15, 1, 17, 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: [13, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 15, 11, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 13, 13, 13, 6, 6, 3, 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522975805 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522975805/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522975805 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 783) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(F)(F)F)c(Br)c2)cc1Cl) `ZINC001522975805.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001522975805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522975805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001522975805 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(F)(F)F)c(Br)c2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'Br', '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, 1, 5, 15, 15, 15, 1, 17, 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: [15, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 15, 9, 15, 15, 15, 15, 15, 15, 15, 6, 6, 6, 15, 15, 15, 6, 6, 3, 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522975805 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001522975805 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522975805/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522975805/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001522975805 Building ZINC001523042284 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042284' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042284 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523042284 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042284/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042284 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/784 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccn2c1nc(c1ccccc1)c2NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001523042284.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523042284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001523042284 none Cc1cccn2c1nc(c1ccccc1)c2NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 8, 1, 1, 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, 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, 4, 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: [22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 34, 34, 22, 34, 34, 15, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 22, 22, 22, 22, 22, 22, 34, 34, 22, 34, 34, 15, 9, 9] 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042284 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042284/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042284 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 785) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/785 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/785' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccn2c1nc(c1ccccc1)c2NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001523042284.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523042284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001523042284 none Cc1cccn2c1nc(c1ccccc1)c2NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 8, 1, 1, 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, 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, 4, 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: [22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 34, 34, 22, 34, 34, 15, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 22, 22, 22, 22, 22, 22, 34, 34, 22, 34, 34, 15, 9, 9] 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042284 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523042284 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042284/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042284/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042284 Building ZINC001523042284 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042284' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042284 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523042284 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042284/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042284 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 784) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1cccn2c1nc(c1ccccc1)c2NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001523042284.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523042284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001523042284 none Cc1cccn2c1nc(c1ccccc1)c2NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 8, 1, 1, 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, 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, 4, 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: [22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 34, 34, 22, 34, 34, 15, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 22, 22, 22, 22, 22, 22, 34, 34, 22, 34, 34, 15, 9, 9] 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042284 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042284/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042284 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 785) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1cccn2c1nc(c1ccccc1)c2NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001523042284.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523042284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042284/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001523042284 none Cc1cccn2c1nc(c1ccccc1)c2NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 8, 1, 1, 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, 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, 4, 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: [22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 34, 34, 22, 34, 34, 15, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 22, 22, 22, 22, 22, 22, 34, 34, 22, 34, 34, 15, 9, 9] 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042284 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523042284 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042284/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042284/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042284 Building ZINC001523042543 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042543' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042543 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523042543 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042543/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042543 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/786 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/786' -> `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)ccc(F)c1Br) `ZINC001523042543.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523042543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001523042543 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(C)ccc(F)c1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'F', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 15, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 13, 13, 4, 4, 1, 1, 1, 1, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 13, 13, 8, 13, 13, 4, 4, 4, 8, 21, 21, 21, 21, 21] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 74 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042543 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042543/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042543 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 787) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/787 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/787' -> `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)ccc(F)c1Br) `ZINC001523042543.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523042543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042543/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001523042543 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(C)ccc(F)c1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'F', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 15, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 7, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 13, 13, 5, 13, 13, 4, 4, 4, 7, 21, 21, 21, 21, 21] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 72 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042543 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523042543 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042543/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042543/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042543 Building ZINC001523042543 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042543' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042543 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523042543 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042543/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042543 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 786) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(C)ccc(F)c1Br) `ZINC001523042543.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523042543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001523042543 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(C)ccc(F)c1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'F', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 15, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 13, 13, 4, 4, 1, 1, 1, 1, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 13, 13, 8, 13, 13, 4, 4, 4, 8, 21, 21, 21, 21, 21] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 74 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042543 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042543/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042543 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 787) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(C)ccc(F)c1Br) `ZINC001523042543.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523042543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042543/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001523042543 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(C)ccc(F)c1Br NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'F', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 15, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 7, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 13, 13, 5, 13, 13, 4, 4, 4, 7, 21, 21, 21, 21, 21] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 72 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042543 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523042543 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042543/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042543/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523042543 Building ZINC001523077975 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001523077975 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/788 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001523077975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523077975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001523077975 none CC(C)C[C@H]1CN(CCCc2ccccc2)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.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 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, 7, 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, 7, 7] 0 hydrogens 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, 5, 5, 5, 5, 5, 5, 14, 23, 34, 34, 34, 34, 34, 34, 5, 5, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 14, 14, 23, 23, 34, 34, 34, 34, 34, 34, 34, 5, 5, 5, 5, 3, 3] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 173 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 789) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/789 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/789' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001523077975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523077975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001523077975 none CC(C)C[C@H]1CN(CCCc2ccccc2)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.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 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, 7, 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, 7, 7] 0 hydrogens 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, 5, 5, 5, 5, 5, 5, 14, 23, 34, 34, 34, 34, 34, 34, 5, 5, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 14, 14, 23, 23, 34, 34, 34, 34, 34, 34, 34, 5, 5, 5, 5, 3, 3] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 173 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 790) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/790 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/790' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001523077975.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001523077975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001523077975 none CC(C)C[C@H]1CN(CCCc2ccccc2)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.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 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, 7, 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, 7, 7] 0 hydrogens 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, 3, 3, 3, 3, 3, 3, 11, 19, 30, 32, 32, 31, 32, 32, 3, 3, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 11, 11, 19, 19, 30, 30, 32, 32, 30, 32, 32, 3, 3, 3, 3, 4, 4] 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, 56, 57]) total number of confs: 166 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 791) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/791 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/791' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001523077975.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001523077975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001523077975 none CC(C)C[C@H]1CN(CCCc2ccccc2)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.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 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, 7, 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, 7, 7] 0 hydrogens 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, 3, 3, 3, 3, 3, 3, 11, 19, 30, 32, 32, 31, 32, 32, 3, 3, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 11, 11, 19, 19, 30, 30, 32, 32, 30, 32, 32, 3, 3, 3, 3, 4, 4] 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, 56, 57]) total number of confs: 166 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523077975 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 Building ZINC001523077975 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001523077975 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 788) grep: /scratch/xiaobo/12845/xbi-8058088.35/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[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001523077975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523077975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001523077975 none CC(C)C[C@H]1CN(CCCc2ccccc2)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.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 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, 7, 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, 7, 7] 0 hydrogens 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, 5, 5, 5, 5, 5, 5, 14, 23, 34, 34, 34, 34, 34, 34, 5, 5, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 14, 14, 23, 23, 34, 34, 34, 34, 34, 34, 34, 5, 5, 5, 5, 3, 3] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 173 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 789) grep: /scratch/xiaobo/12845/xbi-8058088.35/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[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001523077975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523077975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001523077975 none CC(C)C[C@H]1CN(CCCc2ccccc2)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.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 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, 7, 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, 7, 7] 0 hydrogens 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, 5, 5, 5, 5, 5, 5, 14, 23, 34, 34, 34, 34, 34, 34, 5, 5, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 14, 14, 23, 23, 34, 34, 34, 34, 34, 34, 34, 5, 5, 5, 5, 3, 3] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 173 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 790) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/790: 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(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001523077975.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001523077975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001523077975 none CC(C)C[C@H]1CN(CCCc2ccccc2)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.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 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, 7, 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, 7, 7] 0 hydrogens 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, 3, 3, 3, 3, 3, 3, 11, 19, 30, 32, 32, 31, 32, 32, 3, 3, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 11, 11, 19, 19, 30, 30, 32, 32, 30, 32, 32, 3, 3, 3, 3, 4, 4] 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, 56, 57]) total number of confs: 166 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 791) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/791: 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(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001523077975.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001523077975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001523077975 none CC(C)C[C@H]1CN(CCCc2ccccc2)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.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 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, 7, 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, 7, 7] 0 hydrogens 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, 3, 3, 3, 3, 3, 3, 11, 19, 30, 32, 32, 31, 32, 32, 3, 3, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 11, 11, 19, 19, 30, 30, 32, 32, 30, 32, 32, 3, 3, 3, 3, 4, 4] 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, 56, 57]) total number of confs: 166 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523077975 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 Building ZINC001523077975 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001523077975 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 788) grep: /scratch/xiaobo/12845/xbi-8058088.35/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[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001523077975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523077975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001523077975 none CC(C)C[C@H]1CN(CCCc2ccccc2)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.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 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, 7, 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, 7, 7] 0 hydrogens 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, 5, 5, 5, 5, 5, 5, 14, 23, 34, 34, 34, 34, 34, 34, 5, 5, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 14, 14, 23, 23, 34, 34, 34, 34, 34, 34, 34, 5, 5, 5, 5, 3, 3] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 173 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 789) grep: /scratch/xiaobo/12845/xbi-8058088.35/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[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001523077975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523077975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001523077975 none CC(C)C[C@H]1CN(CCCc2ccccc2)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.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 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, 7, 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, 7, 7] 0 hydrogens 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, 5, 5, 5, 5, 5, 5, 14, 23, 34, 34, 34, 34, 34, 34, 5, 5, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 14, 14, 23, 23, 34, 34, 34, 34, 34, 34, 34, 5, 5, 5, 5, 3, 3] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 173 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 790) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/790: 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(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001523077975.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001523077975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001523077975 none CC(C)C[C@H]1CN(CCCc2ccccc2)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.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 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, 7, 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, 7, 7] 0 hydrogens 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, 3, 3, 3, 3, 3, 3, 11, 19, 30, 32, 32, 31, 32, 32, 3, 3, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 11, 11, 19, 19, 30, 30, 32, 32, 30, 32, 32, 3, 3, 3, 3, 4, 4] 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, 56, 57]) total number of confs: 166 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 791) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/791: 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(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001523077975.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001523077975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001523077975 none CC(C)C[C@H]1CN(CCCc2ccccc2)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.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 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, 7, 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, 7, 7] 0 hydrogens 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, 3, 3, 3, 3, 3, 3, 11, 19, 30, 32, 32, 31, 32, 32, 3, 3, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 11, 11, 19, 19, 30, 30, 32, 32, 30, 32, 32, 3, 3, 3, 3, 4, 4] 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, 56, 57]) total number of confs: 166 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523077975 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 Building ZINC001523077975 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001523077975 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 788) grep: /scratch/xiaobo/12845/xbi-8058088.35/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[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001523077975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523077975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001523077975 none CC(C)C[C@H]1CN(CCCc2ccccc2)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.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 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, 7, 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, 7, 7] 0 hydrogens 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, 5, 5, 5, 5, 5, 5, 14, 23, 34, 34, 34, 34, 34, 34, 5, 5, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 14, 14, 23, 23, 34, 34, 34, 34, 34, 34, 34, 5, 5, 5, 5, 3, 3] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 173 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 789) grep: /scratch/xiaobo/12845/xbi-8058088.35/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[C@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001523077975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523077975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001523077975 none CC(C)C[C@H]1CN(CCCc2ccccc2)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.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 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, 7, 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, 7, 7] 0 hydrogens 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, 5, 5, 5, 5, 5, 5, 14, 23, 34, 34, 34, 34, 34, 34, 5, 5, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 14, 14, 23, 23, 34, 34, 34, 34, 34, 34, 34, 5, 5, 5, 5, 3, 3] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 173 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 790) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/790: 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(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001523077975.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001523077975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001523077975 none CC(C)C[C@H]1CN(CCCc2ccccc2)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.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 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, 7, 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, 7, 7] 0 hydrogens 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, 3, 3, 3, 3, 3, 3, 11, 19, 30, 32, 32, 31, 32, 32, 3, 3, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 11, 11, 19, 19, 30, 30, 32, 32, 30, 32, 32, 3, 3, 3, 3, 4, 4] 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, 56, 57]) total number of confs: 166 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 791) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/791: 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(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001523077975.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001523077975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001523077975 none CC(C)C[C@H]1CN(CCCc2ccccc2)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.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 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, 7, 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, 7, 7] 0 hydrogens 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, 3, 3, 3, 3, 3, 3, 11, 19, 30, 32, 32, 31, 32, 32, 3, 3, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 11, 11, 19, 19, 30, 30, 32, 32, 30, 32, 32, 3, 3, 3, 3, 4, 4] 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, 56, 57]) total number of confs: 166 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523077975 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077975 Building ZINC001523077980 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001523077980 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/792 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001523077980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523077980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001523077980 none CC(C)C[C@@H]1CN(CCCc2ccccc2)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.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 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, 7, 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, 7, 7] 0 hydrogens need 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, 4, 4, 8, 15, 30, 30, 30, 30, 30, 30, 4, 4, 4, 2, 4, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 15, 15, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 3, 3] 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, 56, 57]) total number of confs: 147 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 793) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/793 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/793' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001523077980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523077980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001523077980 none CC(C)C[C@@H]1CN(CCCc2ccccc2)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.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 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, 7, 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, 7, 7] 0 hydrogens need 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, 4, 4, 8, 15, 30, 30, 30, 30, 30, 30, 4, 4, 4, 2, 4, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 15, 15, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 3, 3] 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, 56, 57]) total number of confs: 147 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 794) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/794 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/794' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001523077980.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001523077980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001523077980 none CC(C)C[C@@H]1CN(CCCc2ccccc2)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.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 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, 7, 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, 7, 7] 0 hydrogens 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, 6, 15, 22, 34, 34, 34, 34, 34, 34, 6, 6, 5, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 22, 22, 34, 34, 34, 34, 34, 34, 34, 6, 6, 6, 6, 4, 4] 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, 56, 57]) total number of confs: 162 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 795) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/795 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/795' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001523077980.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001523077980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001523077980 none CC(C)C[C@@H]1CN(CCCc2ccccc2)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.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 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, 7, 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, 7, 7] 0 hydrogens 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, 6, 15, 22, 34, 34, 34, 34, 34, 34, 6, 6, 5, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 22, 22, 34, 34, 34, 34, 34, 34, 34, 6, 6, 6, 6, 4, 4] 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, 56, 57]) total number of confs: 162 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523077980 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 Building ZINC001523077980 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001523077980 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 792) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001523077980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523077980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001523077980 none CC(C)C[C@@H]1CN(CCCc2ccccc2)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.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 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, 7, 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, 7, 7] 0 hydrogens need 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, 4, 4, 8, 15, 30, 30, 30, 30, 30, 30, 4, 4, 4, 2, 4, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 15, 15, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 3, 3] 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, 56, 57]) total number of confs: 147 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 793) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001523077980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523077980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001523077980 none CC(C)C[C@@H]1CN(CCCc2ccccc2)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.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 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, 7, 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, 7, 7] 0 hydrogens need 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, 4, 4, 8, 15, 30, 30, 30, 30, 30, 30, 4, 4, 4, 2, 4, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 15, 15, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 3, 3] 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, 56, 57]) total number of confs: 147 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 794) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/794: 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(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001523077980.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001523077980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001523077980 none CC(C)C[C@@H]1CN(CCCc2ccccc2)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.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 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, 7, 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, 7, 7] 0 hydrogens 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, 6, 15, 22, 34, 34, 34, 34, 34, 34, 6, 6, 5, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 22, 22, 34, 34, 34, 34, 34, 34, 34, 6, 6, 6, 6, 4, 4] 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, 56, 57]) total number of confs: 162 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 795) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/795: 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(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001523077980.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001523077980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001523077980 none CC(C)C[C@@H]1CN(CCCc2ccccc2)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.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 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, 7, 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, 7, 7] 0 hydrogens 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, 6, 15, 22, 34, 34, 34, 34, 34, 34, 6, 6, 5, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 22, 22, 34, 34, 34, 34, 34, 34, 34, 6, 6, 6, 6, 4, 4] 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, 56, 57]) total number of confs: 162 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523077980 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 Building ZINC001523077980 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001523077980 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 792) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001523077980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523077980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001523077980 none CC(C)C[C@@H]1CN(CCCc2ccccc2)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.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 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, 7, 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, 7, 7] 0 hydrogens need 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, 4, 4, 8, 15, 30, 30, 30, 30, 30, 30, 4, 4, 4, 2, 4, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 15, 15, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 3, 3] 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, 56, 57]) total number of confs: 147 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 793) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001523077980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523077980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001523077980 none CC(C)C[C@@H]1CN(CCCc2ccccc2)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.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 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, 7, 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, 7, 7] 0 hydrogens need 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, 4, 4, 8, 15, 30, 30, 30, 30, 30, 30, 4, 4, 4, 2, 4, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 15, 15, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 3, 3] 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, 56, 57]) total number of confs: 147 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 794) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/794: 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(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001523077980.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001523077980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001523077980 none CC(C)C[C@@H]1CN(CCCc2ccccc2)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.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 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, 7, 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, 7, 7] 0 hydrogens 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, 6, 15, 22, 34, 34, 34, 34, 34, 34, 6, 6, 5, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 22, 22, 34, 34, 34, 34, 34, 34, 34, 6, 6, 6, 6, 4, 4] 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, 56, 57]) total number of confs: 162 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 795) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/795: 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(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001523077980.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001523077980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001523077980 none CC(C)C[C@@H]1CN(CCCc2ccccc2)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.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 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, 7, 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, 7, 7] 0 hydrogens 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, 6, 15, 22, 34, 34, 34, 34, 34, 34, 6, 6, 5, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 22, 22, 34, 34, 34, 34, 34, 34, 34, 6, 6, 6, 6, 4, 4] 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, 56, 57]) total number of confs: 162 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523077980 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 Building ZINC001523077980 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001523077980 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 792) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001523077980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523077980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001523077980 none CC(C)C[C@@H]1CN(CCCc2ccccc2)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.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 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, 7, 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, 7, 7] 0 hydrogens need 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, 4, 4, 8, 15, 30, 30, 30, 30, 30, 30, 4, 4, 4, 2, 4, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 15, 15, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 3, 3] 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, 56, 57]) total number of confs: 147 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 793) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)C[C@@H]1CN(CCCc2ccccc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001523077980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523077980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001523077980 none CC(C)C[C@@H]1CN(CCCc2ccccc2)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.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 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, 7, 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, 7, 7] 0 hydrogens need 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, 4, 4, 8, 15, 30, 30, 30, 30, 30, 30, 4, 4, 4, 2, 4, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 15, 15, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 3, 3] 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, 56, 57]) total number of confs: 147 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 794) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/794: 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(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001523077980.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001523077980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001523077980 none CC(C)C[C@@H]1CN(CCCc2ccccc2)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.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 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, 7, 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, 7, 7] 0 hydrogens 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, 6, 15, 22, 34, 34, 34, 34, 34, 34, 6, 6, 5, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 22, 22, 34, 34, 34, 34, 34, 34, 34, 6, 6, 6, 6, 4, 4] 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, 56, 57]) total number of confs: 162 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 795) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/795: 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(CCCc2ccccc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001523077980.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001523077980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 61 natoms 60 natoms 59 natoms 58 names: ZINC001523077980 none CC(C)C[C@@H]1CN(CCCc2ccccc2)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.3', 'C.3', '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.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'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 10, 5, 5, 5, 1, 1, 1, 1, 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, 7, 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, 7, 7] 0 hydrogens 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, 6, 15, 22, 34, 34, 34, 34, 34, 34, 6, 6, 5, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 22, 22, 34, 34, 34, 34, 34, 34, 34, 6, 6, 6, 6, 4, 4] 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, 56, 57]) total number of confs: 162 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523077980 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523077980 Building ZINC001523145253 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145253' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145253 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523145253 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145253/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145253 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/796 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2c(cc1OC)[C@H](c1ccccc1)N(C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)CC2) `ZINC001523145253.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523145253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001523145253 none COc1cc2c(cc1OC)[C@H](c1ccccc1)N(C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)CC2 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.3', 'C.3', 'H', '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.3', 'C.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, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [27, 13, 13, 13, 13, 13, 13, 13, 13, 31, 13, 13, 13, 21, 21, 21, 21, 21, 7, 2, 7, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 13, 13, 27, 27, 27, 13, 13, 31, 31, 31, 21, 21, 21, 21, 21, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13] 39 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 100 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145253 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145253/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145253 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 797) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/797 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/797' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2c(cc1OC)[C@H](c1ccccc1)N(C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)CC2) `ZINC001523145253.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523145253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145253/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001523145253 none COc1cc2c(cc1OC)[C@H](c1ccccc1)N(C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)CC2 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.3', 'C.3', 'H', '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.3', 'C.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, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 11, 11, 11, 31, 11, 11, 11, 23, 23, 11, 23, 23, 6, 2, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 11, 11, 27, 27, 27, 11, 11, 31, 31, 31, 23, 23, 11, 23, 23, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 138 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145253 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523145253 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145253/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145253/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145253 Building ZINC001523145253 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145253' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145253 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523145253 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145253/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145253 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 796) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1cc2c(cc1OC)[C@H](c1ccccc1)N(C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)CC2) `ZINC001523145253.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523145253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001523145253 none COc1cc2c(cc1OC)[C@H](c1ccccc1)N(C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)CC2 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.3', 'C.3', 'H', '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.3', 'C.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, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [27, 13, 13, 13, 13, 13, 13, 13, 13, 31, 13, 13, 13, 21, 21, 21, 21, 21, 7, 2, 7, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 13, 13, 27, 27, 27, 13, 13, 31, 31, 31, 21, 21, 21, 21, 21, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13] 39 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 100 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145253 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145253/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145253 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 797) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1cc2c(cc1OC)[C@H](c1ccccc1)N(C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)CC2) `ZINC001523145253.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523145253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145253/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001523145253 none COc1cc2c(cc1OC)[C@H](c1ccccc1)N(C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)CC2 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.3', 'C.3', 'H', '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.3', 'C.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, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 11, 11, 11, 31, 11, 11, 11, 23, 23, 11, 23, 23, 6, 2, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 11, 11, 27, 27, 27, 11, 11, 31, 31, 31, 23, 23, 11, 23, 23, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 138 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145253 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523145253 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145253/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145253/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145253 Building ZINC001523145255 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145255' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145255 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523145255 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145255/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145255 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/798 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2c(cc1OC)[C@@H](c1ccccc1)N(C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)CC2) `ZINC001523145255.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523145255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001523145255 none COc1cc2c(cc1OC)[C@@H](c1ccccc1)N(C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)CC2 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.3', 'C.3', 'H', '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.3', 'C.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, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 13, 13, 13, 13, 13, 13, 13, 13, 36, 13, 13, 13, 24, 24, 13, 24, 24, 8, 2, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 13, 13, 31, 31, 31, 13, 13, 36, 36, 36, 24, 24, 13, 24, 24, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 145 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145255 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145255/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145255 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 799) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/799 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/799' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2c(cc1OC)[C@@H](c1ccccc1)N(C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)CC2) `ZINC001523145255.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523145255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001523145255 none COc1cc2c(cc1OC)[C@@H](c1ccccc1)N(C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)CC2 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.3', 'C.3', 'H', '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.3', 'C.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, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [28, 13, 13, 13, 13, 13, 13, 13, 13, 31, 13, 13, 13, 21, 21, 13, 21, 21, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 13, 13, 28, 28, 28, 13, 13, 31, 31, 31, 21, 21, 13, 21, 21, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13] 40 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 124 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145255 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523145255 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145255/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145255/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145255 Building ZINC001523145255 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145255' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145255 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523145255 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145255/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145255 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 798) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1cc2c(cc1OC)[C@@H](c1ccccc1)N(C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)CC2) `ZINC001523145255.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523145255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001523145255 none COc1cc2c(cc1OC)[C@@H](c1ccccc1)N(C(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C)CC2 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.3', 'C.3', 'H', '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.3', 'C.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, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 13, 13, 13, 13, 13, 13, 13, 13, 36, 13, 13, 13, 24, 24, 13, 24, 24, 8, 2, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 13, 13, 31, 31, 31, 13, 13, 36, 36, 36, 24, 24, 13, 24, 24, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 145 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145255 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145255/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145255 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 799) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1cc2c(cc1OC)[C@@H](c1ccccc1)N(C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)CC2) `ZINC001523145255.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523145255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001523145255 none COc1cc2c(cc1OC)[C@@H](c1ccccc1)N(C(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C)CC2 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.3', 'C.3', 'H', '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.3', 'C.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, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 7, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [28, 13, 13, 13, 13, 13, 13, 13, 13, 31, 13, 13, 13, 21, 21, 13, 21, 21, 7, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 13, 13, 28, 28, 28, 13, 13, 31, 31, 31, 21, 21, 13, 21, 21, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13] 40 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 124 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145255 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523145255 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145255/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145255/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523145255 Building ZINC001523152006 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152006' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152006 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523152006 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152006/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152006 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/800 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(Br)ccc1[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001523152006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523152006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523152006 none COc1cc(Br)ccc1[C@@H](C)NC(=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', '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', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] 0 hydrogens 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, 29, 29, 29, 20, 29, 29, 29, 12, 6, 12, 12, 6, 1, 6, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 36, 36, 36, 29, 29, 29, 12, 12, 12, 6, 5, 1, 5] 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]) total number of confs: 130 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152006 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152006/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152006 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 801) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/801 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/801' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(Br)ccc1[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001523152006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523152006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523152006 none COc1cc(Br)ccc1[C@@H](C)NC(=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', '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', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] 0 hydrogens 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, 30, 30, 30, 18, 30, 30, 30, 11, 6, 11, 11, 6, 1, 6, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 35, 35, 35, 30, 30, 30, 11, 11, 11, 6, 5, 1, 5] 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]) total number of confs: 135 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152006 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523152006 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152006/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152006/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152006 Building ZINC001523152006 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152006' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152006 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523152006 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152006/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152006 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 800) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1cc(Br)ccc1[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001523152006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523152006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523152006 none COc1cc(Br)ccc1[C@@H](C)NC(=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', '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', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] 0 hydrogens 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, 29, 29, 29, 20, 29, 29, 29, 12, 6, 12, 12, 6, 1, 6, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 36, 36, 36, 29, 29, 29, 12, 12, 12, 6, 5, 1, 5] 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]) total number of confs: 130 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152006 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152006/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152006 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 801) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1cc(Br)ccc1[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001523152006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523152006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523152006 none COc1cc(Br)ccc1[C@@H](C)NC(=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', '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', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] 0 hydrogens 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, 30, 30, 30, 18, 30, 30, 30, 11, 6, 11, 11, 6, 1, 6, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 35, 35, 35, 30, 30, 30, 11, 11, 11, 6, 5, 1, 5] 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]) total number of confs: 135 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152006 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523152006 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152006/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152006/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152006 Building ZINC001523152009 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152009' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152009 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523152009 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152009/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152009 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/802 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(Br)ccc1[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001523152009.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523152009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523152009 none COc1cc(Br)ccc1[C@H](C)NC(=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', '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', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] 0 hydrogens 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, 30, 30, 30, 30, 30, 30, 30, 11, 6, 11, 11, 6, 1, 6, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 35, 35, 35, 30, 30, 30, 11, 11, 11, 6, 5, 2, 5] 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: 92 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152009 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152009/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152009 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 803) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/803 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/803' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(Br)ccc1[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001523152009.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523152009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523152009 none COc1cc(Br)ccc1[C@H](C)NC(=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', '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', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] 0 hydrogens 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, 29, 29, 29, 29, 29, 29, 29, 12, 6, 12, 12, 6, 1, 6, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 36, 36, 36, 29, 29, 29, 12, 12, 12, 6, 5, 1, 5] 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]) total number of confs: 97 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152009 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523152009 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152009/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152009/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152009 Building ZINC001523152009 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152009' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152009 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523152009 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152009/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152009 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 802) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1cc(Br)ccc1[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001523152009.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523152009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523152009 none COc1cc(Br)ccc1[C@H](C)NC(=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', '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', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] 0 hydrogens 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, 30, 30, 30, 30, 30, 30, 30, 11, 6, 11, 11, 6, 1, 6, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 35, 35, 35, 30, 30, 30, 11, 11, 11, 6, 5, 2, 5] 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: 92 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152009 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152009/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152009 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 803) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1cc(Br)ccc1[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001523152009.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523152009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523152009 none COc1cc(Br)ccc1[C@H](C)NC(=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', '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', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] 0 hydrogens 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, 29, 29, 29, 29, 29, 29, 29, 12, 6, 12, 12, 6, 1, 6, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 36, 36, 36, 29, 29, 29, 12, 12, 12, 6, 5, 1, 5] 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]) total number of confs: 97 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152009 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523152009 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152009/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152009/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523152009 Building ZINC001523227640 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523227640' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523227640 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523227640 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523227640/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523227640 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/804 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/804' -> `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)N1CCCc2cc(C)ccc21) `ZINC001523227640.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523227640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523227640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001523227640 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCc2cc(C)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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.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'] dock atom type numbers: [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, 5, 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, 27, 27, 8, 27, 27, 27, 27, 27, 27, 4, 4, 1, 1, 1, 3, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 27, 27, 17, 27, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 88 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523227640 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523227640/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523227640 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 805) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/805 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/805' -> `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)N1CCCc2cc(C)ccc21) `ZINC001523227640.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523227640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523227640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001523227640 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCc2cc(C)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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.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'] dock atom type numbers: [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, 5, 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, 27, 27, 4, 27, 27, 27, 27, 27, 27, 4, 4, 1, 1, 1, 3, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 4, 27, 27, 4, 27, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 82 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523227640 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523227640 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523227640/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523227640/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523227640 Building ZINC001523227640 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523227640' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523227640 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523227640 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523227640/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523227640 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 804) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCc2cc(C)ccc21) `ZINC001523227640.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523227640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523227640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001523227640 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCc2cc(C)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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.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'] dock atom type numbers: [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, 5, 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, 27, 27, 8, 27, 27, 27, 27, 27, 27, 4, 4, 1, 1, 1, 3, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 27, 27, 17, 27, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 88 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523227640 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523227640/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523227640 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 805) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCc2cc(C)ccc21) `ZINC001523227640.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523227640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523227640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001523227640 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCc2cc(C)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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.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'] dock atom type numbers: [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, 5, 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, 27, 27, 4, 27, 27, 27, 27, 27, 27, 4, 4, 1, 1, 1, 3, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 4, 27, 27, 4, 27, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 82 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523227640 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523227640 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523227640/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523227640/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523227640 Building ZINC001523275576 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523275576' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523275576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523275576 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523275576/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523275576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/806 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(Br)s2)cs1) `ZINC001523275576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523275576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523275576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001523275576 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(Br)s2)cs1 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.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'S.3', '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, 1, 1, 1, 17, 14, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 7, 14, 14, 14, 45, 45, 45, 45, 45, 14, 14, 4, 4, 4, 4, 4, 4, 7, 45, 45, 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]) total number of confs: 74 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523275576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523275576/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523275576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 807) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/807 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/807' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(Br)s2)cs1) `ZINC001523275576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523275576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523275576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001523275576 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(Br)s2)cs1 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.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'S.3', '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, 1, 1, 1, 17, 14, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 7, 14, 14, 14, 44, 44, 44, 44, 44, 14, 14, 4, 4, 4, 4, 4, 4, 7, 44, 44, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 72 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523275576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523275576 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523275576/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523275576/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523275576 Building ZINC001523275576 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523275576' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523275576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523275576 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523275576/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523275576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 806) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(Br)s2)cs1) `ZINC001523275576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523275576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523275576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001523275576 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(Br)s2)cs1 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.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'S.3', '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, 1, 1, 1, 17, 14, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 7, 14, 14, 14, 45, 45, 45, 45, 45, 14, 14, 4, 4, 4, 4, 4, 4, 7, 45, 45, 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]) total number of confs: 74 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523275576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523275576/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523275576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 807) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(Br)s2)cs1) `ZINC001523275576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523275576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523275576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001523275576 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1nc(c2ccc(Br)s2)cs1 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.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'S.3', '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, 1, 1, 1, 17, 14, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 7, 14, 14, 14, 44, 44, 44, 44, 44, 14, 14, 4, 4, 4, 4, 4, 4, 7, 44, 44, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 72 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523275576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523275576 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523275576/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523275576/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523275576 Building ZINC001523281620 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523281620' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523281620 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523281620 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523281620/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523281620 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/808 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(Br)cc1F) `ZINC001523281620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523281620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523281620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001523281620 none COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(Br)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 17, 1, 1, 15, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 36, 13, 38, 13, 13, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 13, 13, 13, 13, 13, 38, 38, 38, 13, 4, 3, 1, 3, 13] 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523281620 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523281620/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523281620 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 809) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/809 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/809' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(Br)cc1F) `ZINC001523281620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523281620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523281620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001523281620 none COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(Br)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 17, 1, 1, 15, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 36, 13, 38, 13, 13, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 13, 13, 13, 13, 13, 38, 38, 38, 13, 4, 3, 1, 3, 13] 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523281620 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523281620 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523281620/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523281620/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523281620 Building ZINC001523281620 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523281620' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523281620 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523281620 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523281620/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523281620 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 808) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(Br)cc1F) `ZINC001523281620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523281620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523281620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001523281620 none COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(Br)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 17, 1, 1, 15, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 36, 13, 38, 13, 13, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 13, 13, 13, 13, 13, 38, 38, 38, 13, 4, 3, 1, 3, 13] 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523281620 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523281620/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523281620 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 809) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(Br)cc1F) `ZINC001523281620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523281620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523281620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001523281620 none COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(Br)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 17, 1, 1, 15, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 36, 13, 38, 13, 13, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 13, 13, 13, 13, 13, 38, 38, 38, 13, 4, 3, 1, 3, 13] 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523281620 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523281620 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523281620/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523281620/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523281620 Building ZINC001523288950 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523288950' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523288950 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523288950 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523288950/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523288950 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/810 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c(OCc2ccccc2)c1) `ZINC001523288950.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523288950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523288950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC001523288950 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c(OCc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 4, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 11, 27, 37, 37, 32, 37, 37, 5, 9, 9, 9, 5, 5, 2, 4, 4, 27, 27, 37, 37, 37, 37, 37, 5] 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]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523288950 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523288950/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523288950 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 811) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/811 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/811' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c(OCc2ccccc2)c1) `ZINC001523288950.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523288950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523288950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC001523288950 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c(OCc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 4, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 11, 27, 38, 38, 33, 38, 38, 5, 9, 9, 9, 5, 5, 2, 4, 4, 27, 27, 38, 38, 38, 38, 38, 5] 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]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523288950 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523288950 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523288950/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523288950/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523288950 Building ZINC001523288950 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523288950' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523288950 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523288950 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523288950/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523288950 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 810) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c(OCc2ccccc2)c1) `ZINC001523288950.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523288950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523288950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC001523288950 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c(OCc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 4, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 11, 27, 37, 37, 32, 37, 37, 5, 9, 9, 9, 5, 5, 2, 4, 4, 27, 27, 37, 37, 37, 37, 37, 5] 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]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523288950 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523288950/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523288950 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 811) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c(OCc2ccccc2)c1) `ZINC001523288950.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523288950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523288950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC001523288950 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c(OCc2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'O.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 4, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 11, 27, 38, 38, 33, 38, 38, 5, 9, 9, 9, 5, 5, 2, 4, 4, 27, 27, 38, 38, 38, 38, 38, 5] 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]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523288950 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523288950 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523288950/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523288950/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523288950 Building ZINC001523303862 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523303862' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523303862 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523303862 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523303862/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523303862 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/812 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(c2ccccc2)nc2ccccn21)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001523303862.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523303862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523303862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001523303862 none O=C(Nc1c(c2ccccc2)nc2ccccn21)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 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, 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] 0 hydrogens 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, 14, 20, 20, 35, 35, 31, 35, 35, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 8, 8, 8, 8, 8, 14, 35, 35, 31, 35, 35, 20, 20, 20, 20, 8, 8] 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]) total number of confs: 92 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523303862 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523303862/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523303862 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 813) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/813 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/813' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(c2ccccc2)nc2ccccn21)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001523303862.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523303862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523303862/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001523303862 none O=C(Nc1c(c2ccccc2)nc2ccccn21)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 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, 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] 0 hydrogens 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, 14, 21, 21, 36, 36, 21, 36, 36, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 8, 8, 8, 8, 8, 14, 36, 36, 21, 36, 36, 21, 21, 21, 21, 8, 8] 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]) total number of confs: 125 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523303862 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523303862 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523303862/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523303862/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523303862 Building ZINC001523303862 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523303862' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523303862 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523303862 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523303862/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523303862 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 812) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1c(c2ccccc2)nc2ccccn21)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001523303862.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523303862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523303862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001523303862 none O=C(Nc1c(c2ccccc2)nc2ccccn21)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 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, 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] 0 hydrogens 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, 14, 20, 20, 35, 35, 31, 35, 35, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 8, 8, 8, 8, 8, 14, 35, 35, 31, 35, 35, 20, 20, 20, 20, 8, 8] 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]) total number of confs: 92 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523303862 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523303862/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523303862 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 813) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1c(c2ccccc2)nc2ccccn21)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001523303862.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523303862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523303862/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001523303862 none O=C(Nc1c(c2ccccc2)nc2ccccn21)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 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, 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] 0 hydrogens 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, 14, 21, 21, 36, 36, 21, 36, 36, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 8, 8, 8, 8, 8, 14, 36, 36, 21, 36, 36, 21, 21, 21, 21, 8, 8] 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]) total number of confs: 125 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523303862 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523303862 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523303862/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523303862/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523303862 Building ZINC001523352105 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352105' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352105 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523352105 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352105/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352105 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/814 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)sc2c1CC[C@@H](C)C2) `ZINC001523352105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523352105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523352105 none CCOC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)sc2c1CC[C@@H](C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', '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', 'S.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 14, 1, 1, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 11, 6, 11, 6, 4, 4, 1, 4, 1, 1, 1, 6, 6, 2, 6, 11, 6, 6, 6, 6, 11, 6, 11, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 4, 6, 6, 11, 11, 11, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352105 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352105/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352105 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 815) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/815 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/815' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)sc2c1CC[C@@H](C)C2) `ZINC001523352105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523352105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523352105 none CCOC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)sc2c1CC[C@@H](C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', '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', 'S.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 14, 1, 1, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 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, 7, 7] 0 hydrogens 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, 11, 11, 6, 11, 6, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 5, 6, 11, 6, 11, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 4, 5, 5, 10, 10, 10, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352105 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523352105 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352105/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352105/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352105 Building ZINC001523352105 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352105' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352105 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523352105 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352105/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352105 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 814) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)sc2c1CC[C@@H](C)C2) `ZINC001523352105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523352105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523352105 none CCOC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)sc2c1CC[C@@H](C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', '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', 'S.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 14, 1, 1, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 11, 6, 11, 6, 4, 4, 1, 4, 1, 1, 1, 6, 6, 2, 6, 11, 6, 6, 6, 6, 11, 6, 11, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 4, 6, 6, 11, 11, 11, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352105 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352105/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352105 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 815) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)sc2c1CC[C@@H](C)C2) `ZINC001523352105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523352105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523352105 none CCOC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)sc2c1CC[C@@H](C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', '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', 'S.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 14, 1, 1, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 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, 7, 7] 0 hydrogens 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, 11, 11, 6, 11, 6, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 10, 5, 5, 5, 6, 11, 6, 11, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 4, 5, 5, 10, 10, 10, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352105 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523352105 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352105/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352105/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352105 Building ZINC001523352107 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352107' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352107 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523352107 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352107/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352107 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/816 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)sc2c1CC[C@H](C)C2) `ZINC001523352107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523352107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523352107 none CCOC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)sc2c1CC[C@H](C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', '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', 'S.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 14, 1, 1, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 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, 7, 7] 0 hydrogens 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, 18, 10, 18, 6, 4, 4, 1, 4, 1, 1, 1, 6, 6, 2, 6, 11, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 4, 6, 6, 11, 11, 11, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352107 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352107/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352107 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 817) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/817 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/817' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)sc2c1CC[C@H](C)C2) `ZINC001523352107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523352107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523352107 none CCOC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)sc2c1CC[C@H](C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', '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', 'S.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 14, 1, 1, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 19, 19, 11, 19, 6, 4, 4, 1, 4, 1, 1, 1, 6, 6, 2, 6, 11, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 4, 6, 6, 11, 11, 11, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352107 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523352107 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352107/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352107/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352107 Building ZINC001523352107 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352107' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352107 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523352107 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352107/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352107 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 816) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)sc2c1CC[C@H](C)C2) `ZINC001523352107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523352107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523352107 none CCOC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)sc2c1CC[C@H](C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', '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', 'S.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 14, 1, 1, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 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, 7, 7] 0 hydrogens 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, 18, 10, 18, 6, 4, 4, 1, 4, 1, 1, 1, 6, 6, 2, 6, 11, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 4, 6, 6, 11, 11, 11, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352107 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352107/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352107 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 817) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)sc2c1CC[C@H](C)C2) `ZINC001523352107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523352107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523352107 none CCOC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)sc2c1CC[C@H](C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', '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', 'S.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 14, 1, 1, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 19, 19, 11, 19, 6, 4, 4, 1, 4, 1, 1, 1, 6, 6, 2, 6, 11, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 4, 6, 6, 11, 11, 11, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11] 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: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352107 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523352107 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352107/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352107/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523352107 Building ZINC001523368442 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523368442' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523368442 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523368442 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523368442/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523368442 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/818 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Br) `ZINC001523368442.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523368442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523368442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523368442 none CN(C)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 10, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 17, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 13, 8, 13, 13, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 13, 13, 13, 36, 36, 36, 36, 36, 36, 36, 36, 13, 13, 2, 3, 1, 3, 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]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523368442 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523368442/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523368442 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 819) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/819 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/819' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Br) `ZINC001523368442.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523368442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523368442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523368442 none CN(C)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 10, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 17, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 8, 12, 12, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 12, 12, 12, 35, 35, 35, 35, 35, 35, 35, 35, 12, 12, 2, 3, 1, 3, 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]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523368442 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523368442 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523368442/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523368442/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523368442 Building ZINC001523368442 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523368442' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523368442 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523368442 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523368442/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523368442 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 818) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CN(C)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Br) `ZINC001523368442.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523368442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523368442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523368442 none CN(C)Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 10, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 17, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 13, 8, 13, 13, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 13, 13, 13, 36, 36, 36, 36, 36, 36, 36, 36, 13, 13, 2, 3, 1, 3, 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]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523368442 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523368442/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523368442 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 819) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CN(C)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Br) `ZINC001523368442.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523368442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523368442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523368442 none CN(C)Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 10, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 17, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 8, 12, 12, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 12, 12, 12, 35, 35, 35, 35, 35, 35, 35, 35, 12, 12, 2, 3, 1, 3, 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]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523368442 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523368442 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523368442/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523368442/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523368442 Building ZINC001523401409 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523401409' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523401409 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523401409 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523401409/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523401409 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/820 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnc(Oc2ccccc2Br)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001523401409.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523401409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523401409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001523401409 none O=C(Nc1ccnc(Oc2ccccc2Br)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 8, 1, 12, 1, 1, 1, 1, 1, 1, 17, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 18, 27, 27, 27, 27, 27, 27, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 5, 5, 27, 27, 27, 27, 5, 4, 4, 4, 4, 4, 4, 4, 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, 41, 42, 43, 44]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523401409 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523401409/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523401409 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 821) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/821 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/821' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnc(Oc2ccccc2Br)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001523401409.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523401409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523401409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001523401409 none O=C(Nc1ccnc(Oc2ccccc2Br)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 8, 1, 12, 1, 1, 1, 1, 1, 1, 17, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 19, 27, 27, 19, 27, 27, 27, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 5, 5, 27, 27, 27, 27, 5, 4, 4, 4, 4, 4, 4, 4, 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, 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/12845/xbi-8058088.35/working/building/ZINC001523401409 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523401409 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523401409/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523401409/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523401409 Building ZINC001523401409 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523401409' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523401409 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523401409 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523401409/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523401409 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 820) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ccnc(Oc2ccccc2Br)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001523401409.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523401409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523401409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001523401409 none O=C(Nc1ccnc(Oc2ccccc2Br)c1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 8, 1, 12, 1, 1, 1, 1, 1, 1, 17, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 18, 27, 27, 27, 27, 27, 27, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 5, 5, 27, 27, 27, 27, 5, 4, 4, 4, 4, 4, 4, 4, 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, 41, 42, 43, 44]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523401409 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523401409/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523401409 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 821) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ccnc(Oc2ccccc2Br)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001523401409.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523401409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523401409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001523401409 none O=C(Nc1ccnc(Oc2ccccc2Br)c1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 1, 8, 1, 12, 1, 1, 1, 1, 1, 1, 17, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 19, 27, 27, 19, 27, 27, 27, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 5, 5, 27, 27, 27, 27, 5, 4, 4, 4, 4, 4, 4, 4, 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, 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/12845/xbi-8058088.35/working/building/ZINC001523401409 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523401409 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523401409/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523401409/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523401409 Building ZINC001523503898 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503898' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503898 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523503898 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503898/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503898 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/822 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](Cc1cccc2ccccc21)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001523503898.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523503898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523503898 none CCOC(=O)[C@H](Cc1cccc2ccccc21)NC(=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.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.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 8, 20, 2, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 36, 36, 36, 36, 36, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 3, 1, 3] 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]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503898 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503898/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503898 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 823) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/823 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/823' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](Cc1cccc2ccccc21)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001523503898.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523503898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523503898 none CCOC(=O)[C@H](Cc1cccc2ccccc21)NC(=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.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.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 19, 9, 19, 3, 9, 9, 22, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 37, 37, 37, 37, 37, 22, 22, 23, 23, 23, 23, 23, 23, 23, 3, 3, 1, 3] 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]) total number of confs: 224 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503898 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523503898 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503898/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503898/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503898 Building ZINC001523503898 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503898' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503898 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523503898 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503898/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503898 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 822) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOC(=O)[C@H](Cc1cccc2ccccc21)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001523503898.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523503898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523503898 none CCOC(=O)[C@H](Cc1cccc2ccccc21)NC(=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.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.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 8, 20, 2, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 36, 36, 36, 36, 36, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 3, 1, 3] 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]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503898 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503898/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503898 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 823) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOC(=O)[C@H](Cc1cccc2ccccc21)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001523503898.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523503898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523503898 none CCOC(=O)[C@H](Cc1cccc2ccccc21)NC(=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.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.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 19, 9, 19, 3, 9, 9, 22, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 37, 37, 37, 37, 37, 22, 22, 23, 23, 23, 23, 23, 23, 23, 3, 3, 1, 3] 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]) total number of confs: 224 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503898 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523503898 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503898/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503898/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503898 Building ZINC001523503901 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503901' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503901 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523503901 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503901/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503901 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/824 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](Cc1cccc2ccccc21)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001523503901.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523503901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523503901 none CCOC(=O)[C@@H](Cc1cccc2ccccc21)NC(=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.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.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 20, 9, 20, 3, 9, 9, 22, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 38, 38, 38, 38, 38, 22, 22, 23, 23, 23, 23, 23, 23, 23, 3, 3, 1, 3] 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]) total number of confs: 223 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503901 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503901/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503901 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 825) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/825 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/825' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](Cc1cccc2ccccc21)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001523503901.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523503901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503901/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523503901 none CCOC(=O)[C@@H](Cc1cccc2ccccc21)NC(=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.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.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 19, 19, 8, 19, 2, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 35, 35, 35, 35, 35, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 3, 1, 3] 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]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503901 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523503901 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503901/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503901/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503901 Building ZINC001523503901 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503901' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503901 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523503901 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503901/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503901 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 824) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOC(=O)[C@@H](Cc1cccc2ccccc21)NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001523503901.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523503901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523503901 none CCOC(=O)[C@@H](Cc1cccc2ccccc21)NC(=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.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.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 20, 9, 20, 3, 9, 9, 22, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 38, 38, 38, 38, 38, 22, 22, 23, 23, 23, 23, 23, 23, 23, 3, 3, 1, 3] 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]) total number of confs: 223 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503901 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503901/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503901 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 825) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOC(=O)[C@@H](Cc1cccc2ccccc21)NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001523503901.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523503901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503901/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523503901 none CCOC(=O)[C@@H](Cc1cccc2ccccc21)NC(=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.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.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 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, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 19, 19, 8, 19, 2, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 35, 35, 35, 35, 35, 21, 21, 21, 21, 21, 21, 21, 21, 21, 2, 3, 1, 3] 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]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503901 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523503901 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503901/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503901/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523503901 Building ZINC001523681404 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523681404' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523681404 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523681404 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523681404/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523681404 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/826 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)Oc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c(C(F)(F)F)c1) `ZINC001523681404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523681404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523681404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001523681404 none CC(C)(C)Oc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c(C(F)(F)F)c1 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', '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', '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, 5, 5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 16, 26, 26, 8, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 8, 8, 2, 6, 6, 6, 6, 6, 6, 6, 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, 50, 51, 52, 53]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523681404 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523681404/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523681404 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 827) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/827 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/827' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)Oc1ccc(CNC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c(C(F)(F)F)c1) `ZINC001523681404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523681404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523681404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001523681404 none CC(C)(C)Oc1ccc(CNC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c(C(F)(F)F)c1 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', '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', '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, 5, 5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 7, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 25, 25, 25, 25, 25, 25, 25, 25, 25, 7, 7, 7, 7, 2, 7, 7, 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, 50, 51, 52, 53]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523681404 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523681404 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523681404/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523681404/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523681404 Building ZINC001523681404 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523681404' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523681404 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523681404 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523681404/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523681404 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 826) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)Oc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c(C(F)(F)F)c1) `ZINC001523681404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523681404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523681404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001523681404 none CC(C)(C)Oc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c(C(F)(F)F)c1 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', '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', '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, 5, 5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 16, 26, 26, 8, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 8, 8, 2, 6, 6, 6, 6, 6, 6, 6, 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, 50, 51, 52, 53]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523681404 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523681404/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523681404 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 827) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC(C)(C)Oc1ccc(CNC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c(C(F)(F)F)c1) `ZINC001523681404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523681404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523681404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001523681404 none CC(C)(C)Oc1ccc(CNC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c(C(F)(F)F)c1 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', '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', '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, 5, 5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 7, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 25, 25, 25, 25, 25, 25, 25, 25, 25, 7, 7, 7, 7, 2, 7, 7, 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, 50, 51, 52, 53]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523681404 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523681404 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523681404/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523681404/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523681404 Building ZINC001523689655 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523689655' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523689655 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523689655 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523689655/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523689655 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/828 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)c1ccccc1F) `ZINC001523689655.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523689655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523689655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001523689655 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)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.3', 'F', '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', '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, 1, 1, 1, 1, 1, 1, 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: [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, 14, 14, 14, 14, 14, 14, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14] 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: 42 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523689655 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523689655/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523689655 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 829) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/829 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/829' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)c1ccccc1F) `ZINC001523689655.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523689655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523689655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001523689655 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)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.3', 'F', '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', '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, 1, 1, 1, 1, 1, 1, 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: [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, 14, 14, 9, 14, 14, 14, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14] 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: 55 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523689655 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523689655 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523689655/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523689655/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523689655 Building ZINC001523689655 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523689655' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523689655 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523689655 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523689655/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523689655 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 828) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/828: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)c1ccccc1F) `ZINC001523689655.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523689655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523689655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001523689655 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC(C)(C)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.3', 'F', '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', '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, 1, 1, 1, 1, 1, 1, 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: [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, 14, 14, 14, 14, 14, 14, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14] 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: 42 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523689655 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523689655/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523689655 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 829) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/829: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)c1ccccc1F) `ZINC001523689655.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523689655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523689655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001523689655 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC(C)(C)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.3', 'F', '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', '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, 1, 1, 1, 1, 1, 1, 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: [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, 14, 14, 9, 14, 14, 14, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14] 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: 55 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523689655 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523689655 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523689655/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523689655/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523689655 Building ZINC001523693538 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523693538' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523693538 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523693538 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523693538/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523693538 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/830 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(N(C)C)c(C)c1) `ZINC001523693538.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523693538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523693538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001523693538 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(N(C)C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 8, 5, 5, 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] 0 hydrogens need rotated 50 conformations in 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, 10, 10, 3, 9, 10, 10, 10, 10, 10, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523693538 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523693538/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523693538 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 831) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/831 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/831' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(N(C)C)c(C)c1) `ZINC001523693538.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523693538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523693538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001523693538 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(N(C)C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 8, 5, 5, 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] 0 hydrogens need 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, 15, 15, 4, 15, 15, 15, 15, 15, 15, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 9, 2, 2, 9, 9, 9, 9, 9, 4, 4, 4, 15, 15, 4, 15, 4, 4, 4, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523693538 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523693538 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523693538/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523693538/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523693538 Building ZINC001523693538 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523693538' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523693538 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523693538 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523693538/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523693538 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 830) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(N(C)C)c(C)c1) `ZINC001523693538.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523693538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523693538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001523693538 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(N(C)C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 8, 5, 5, 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] 0 hydrogens need rotated 50 conformations in 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, 10, 10, 3, 9, 10, 10, 10, 10, 10, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523693538 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523693538/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523693538 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 831) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(N(C)C)c(C)c1) `ZINC001523693538.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523693538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523693538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001523693538 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(N(C)C)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 8, 5, 5, 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] 0 hydrogens need 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, 15, 15, 4, 15, 15, 15, 15, 15, 15, 4, 4, 1, 1, 1, 1, 2, 2, 2, 9, 9, 2, 2, 9, 9, 9, 9, 9, 4, 4, 4, 15, 15, 4, 15, 4, 4, 4, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523693538 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523693538 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523693538/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523693538/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523693538 Building ZINC001523782556 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523782556' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523782556 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523782556 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523782556/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523782556 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/832 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCOc1ccc(Br)cc1)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001523782556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523782556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523782556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523782556 none CCN(CCOc1ccc(Br)cc1)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 5, 8, 5, 5, 12, 1, 1, 1, 1, 17, 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] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 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, 5, 2, 5, 11, 14, 39, 42, 42, 39, 40, 42, 42, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 7, 7, 7, 11, 11, 14, 14, 42, 42, 42, 42, 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, 37, 38, 39, 40]) total number of confs: 130 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523782556 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523782556/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523782556 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 833) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/833 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/833' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCOc1ccc(Br)cc1)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001523782556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523782556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523782556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523782556 none CCN(CCOc1ccc(Br)cc1)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 5, 8, 5, 5, 12, 1, 1, 1, 1, 17, 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] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 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, 5, 2, 5, 12, 15, 41, 44, 44, 41, 41, 44, 44, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 7, 7, 7, 12, 12, 15, 15, 44, 44, 44, 44, 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, 37, 38, 39, 40]) total number of confs: 134 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523782556 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523782556 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523782556/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523782556/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523782556 Building ZINC001523782556 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523782556' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523782556 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523782556 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523782556/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523782556 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 832) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCN(CCOc1ccc(Br)cc1)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001523782556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523782556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523782556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523782556 none CCN(CCOc1ccc(Br)cc1)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 5, 8, 5, 5, 12, 1, 1, 1, 1, 17, 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] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 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, 5, 2, 5, 11, 14, 39, 42, 42, 39, 40, 42, 42, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 7, 7, 7, 11, 11, 14, 14, 42, 42, 42, 42, 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, 37, 38, 39, 40]) total number of confs: 130 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523782556 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523782556/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523782556 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 833) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCN(CCOc1ccc(Br)cc1)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001523782556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523782556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523782556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523782556 none CCN(CCOc1ccc(Br)cc1)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 5, 8, 5, 5, 12, 1, 1, 1, 1, 17, 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] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 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, 5, 2, 5, 12, 15, 41, 44, 44, 41, 41, 44, 44, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 7, 7, 7, 7, 7, 12, 12, 15, 15, 44, 44, 44, 44, 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, 37, 38, 39, 40]) total number of confs: 134 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523782556 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523782556 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523782556/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523782556/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523782556 Building ZINC001523797583 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797583' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523797583 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797583/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/834 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CC[C@H](CC)C2) `ZINC001523797583.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523797583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523797583 none CCOC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CC[C@H](CC)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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', 'S.3', 'C.2', 'C.2', '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, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 1, 1, 5, 5, 5, 7, 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, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 12, 23, 7, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 7, 12, 12, 12, 12, 12, 12, 12, 16, 12, 30, 30, 30, 30, 30, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 16, 16, 16, 16, 16, 12, 12] 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: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797583/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 835) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/835 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/835' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CC[C@H](CC)C2) `ZINC001523797583.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523797583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797583/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523797583 none CCOC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CC[C@H](CC)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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', 'S.3', 'C.2', 'C.2', '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, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 1, 1, 5, 5, 5, 7, 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, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 24, 24, 12, 24, 7, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 12, 12, 12, 12, 12, 12, 12, 15, 12, 32, 32, 32, 32, 32, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 15, 15, 15, 15, 15, 12, 12] 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: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523797583 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797583/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797583/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797583 Building ZINC001523797583 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797583' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523797583 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797583/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 834) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CC[C@H](CC)C2) `ZINC001523797583.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523797583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523797583 none CCOC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CC[C@H](CC)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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', 'S.3', 'C.2', 'C.2', '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, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 1, 1, 5, 5, 5, 7, 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, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 12, 23, 7, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 7, 12, 12, 12, 12, 12, 12, 12, 16, 12, 30, 30, 30, 30, 30, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 16, 16, 16, 16, 16, 12, 12] 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: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797583/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 835) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CC[C@H](CC)C2) `ZINC001523797583.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523797583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797583/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523797583 none CCOC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CC[C@H](CC)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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', 'S.3', 'C.2', 'C.2', '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, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 1, 1, 5, 5, 5, 7, 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, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 24, 24, 12, 24, 7, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 12, 12, 12, 12, 12, 12, 12, 15, 12, 32, 32, 32, 32, 32, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 15, 15, 15, 15, 15, 12, 12] 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: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523797583 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797583/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797583/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797583 Building ZINC001523797584 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797584' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797584 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523797584 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797584/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797584 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/836 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CC[C@@H](CC)C2) `ZINC001523797584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523797584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523797584 none CCOC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CC[C@@H](CC)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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', 'S.3', 'C.2', 'C.2', '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, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 1, 1, 5, 5, 5, 7, 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, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 7, 15, 7, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 12, 7, 12, 12, 12, 12, 12, 15, 12, 24, 24, 24, 24, 24, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 15, 15, 15, 15, 15, 12, 12] 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: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797584 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797584/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797584 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 837) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/837 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/837' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CC[C@@H](CC)C2) `ZINC001523797584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523797584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523797584 none CCOC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CC[C@@H](CC)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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', 'S.3', 'C.2', 'C.2', '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, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 1, 1, 5, 5, 5, 7, 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, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 16, 16, 7, 16, 7, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 12, 7, 12, 12, 12, 12, 12, 17, 12, 23, 23, 23, 23, 23, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 17, 17, 17, 17, 17, 12, 12] 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797584 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523797584 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797584/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797584/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797584 Building ZINC001523797584 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797584' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797584 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523797584 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797584/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797584 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 836) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CC[C@@H](CC)C2) `ZINC001523797584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523797584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523797584 none CCOC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CC[C@@H](CC)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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', 'S.3', 'C.2', 'C.2', '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, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 1, 1, 5, 5, 5, 7, 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, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 15, 7, 15, 7, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 12, 7, 12, 12, 12, 12, 12, 15, 12, 24, 24, 24, 24, 24, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 15, 15, 15, 15, 15, 12, 12] 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: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797584 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797584/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797584 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 837) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CC[C@@H](CC)C2) `ZINC001523797584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523797584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523797584 none CCOC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)sc2c1CC[C@@H](CC)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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', 'S.3', 'C.2', 'C.2', '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, 5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 1, 1, 5, 5, 5, 7, 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, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 16, 16, 7, 16, 7, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 12, 7, 12, 12, 12, 12, 12, 17, 12, 23, 23, 23, 23, 23, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 17, 17, 17, 17, 17, 12, 12] 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797584 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523797584 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797584/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797584/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523797584 Building ZINC001523872194 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523872194' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523872194 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523872194 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523872194/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523872194 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/838 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1ccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)n(c3ccccc3)n2)cc1) `ZINC001523872194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523872194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523872194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001523872194 none CCCc1ccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)n(c3ccccc3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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.3', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 14, 32, 32, 9, 9, 9, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 9, 9, 10, 10, 9, 10, 10, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 9, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 9, 10, 10, 32, 32] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 126 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523872194 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523872194/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523872194 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 839) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/839 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/839' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1ccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)n(c3ccccc3)n2)cc1) `ZINC001523872194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523872194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523872194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001523872194 none CCCc1ccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)n(c3ccccc3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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.3', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 33, 32, 8, 8, 8, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 8, 9, 9, 8, 9, 9, 8, 33, 33, 35, 35, 35, 35, 35, 33, 33, 33, 33, 8, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 8, 9, 9, 33, 33] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 212 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523872194 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523872194 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523872194/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523872194/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523872194 Building ZINC001523872194 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523872194' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523872194 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523872194 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523872194/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523872194 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 838) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCCc1ccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)n(c3ccccc3)n2)cc1) `ZINC001523872194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523872194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523872194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001523872194 none CCCc1ccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)n(c3ccccc3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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.3', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 14, 32, 32, 9, 9, 9, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 9, 9, 10, 10, 9, 10, 10, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 9, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 9, 10, 10, 32, 32] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 126 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523872194 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523872194/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523872194 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 839) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCCc1ccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)n(c3ccccc3)n2)cc1) `ZINC001523872194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523872194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523872194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001523872194 none CCCc1ccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)n(c3ccccc3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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.3', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 33, 32, 8, 8, 8, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 8, 9, 9, 8, 9, 9, 8, 33, 33, 35, 35, 35, 35, 35, 33, 33, 33, 33, 8, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 8, 9, 9, 33, 33] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 212 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523872194 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523872194 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523872194/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523872194/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523872194 Building ZINC001523898842 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523898842' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523898842 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523898842 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523898842/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523898842 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/840 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1ccc(Br)cc1Cl)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001523898842.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523898842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523898842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001523898842 none O=C(NCCc1ccc(Br)cc1Cl)[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', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.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, 1, 17, 1, 1, 16, 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, 15, 34, 44, 44, 34, 44, 44, 44, 44, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 15, 15, 34, 34, 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: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523898842 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523898842/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523898842 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 841) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/841 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/841' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1ccc(Br)cc1Cl)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001523898842.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523898842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523898842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001523898842 none O=C(NCCc1ccc(Br)cc1Cl)[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', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.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, 1, 17, 1, 1, 16, 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, 15, 34, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 15, 15, 34, 34, 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: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523898842 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523898842 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523898842/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523898842/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523898842 Building ZINC001523898842 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523898842' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523898842 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523898842 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523898842/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523898842 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 840) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NCCc1ccc(Br)cc1Cl)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001523898842.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523898842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523898842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001523898842 none O=C(NCCc1ccc(Br)cc1Cl)[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', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.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, 1, 17, 1, 1, 16, 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, 15, 34, 44, 44, 34, 44, 44, 44, 44, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 15, 15, 34, 34, 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: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523898842 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523898842/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523898842 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 841) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NCCc1ccc(Br)cc1Cl)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001523898842.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523898842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523898842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001523898842 none O=C(NCCc1ccc(Br)cc1Cl)[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', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.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, 1, 17, 1, 1, 16, 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, 15, 34, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 15, 15, 34, 34, 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: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523898842 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523898842 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523898842/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523898842/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523898842 Building ZINC001523918082 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918082' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918082 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523918082 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918082/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918082 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/842 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)N2CCCCC2)cc1) `ZINC001523918082.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523918082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523918082 none COc1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)N2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 29, 42, 42, 29, 14, 29, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 32, 37, 37, 37, 37, 37, 42, 42, 42, 42, 42, 42, 42, 14, 14, 4, 3, 1, 3, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 42, 42] 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: 215 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918082 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918082/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918082 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 843) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/843 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/843' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)N2CCCCC2)cc1) `ZINC001523918082.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523918082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523918082 none COc1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)N2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 31, 40, 40, 31, 15, 31, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 36, 39, 39, 39, 39, 39, 40, 40, 40, 40, 40, 40, 40, 15, 15, 3, 3, 1, 3, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 40, 40] 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: 199 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918082 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523918082 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918082/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918082/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918082 Building ZINC001523918082 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918082' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918082 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523918082 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918082/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918082 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 842) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)N2CCCCC2)cc1) `ZINC001523918082.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523918082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523918082 none COc1ccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)N2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 29, 42, 42, 29, 14, 29, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 32, 37, 37, 37, 37, 37, 42, 42, 42, 42, 42, 42, 42, 14, 14, 4, 3, 1, 3, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 42, 42] 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: 215 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918082 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918082/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918082 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 843) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)N2CCCCC2)cc1) `ZINC001523918082.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523918082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523918082 none COc1ccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)N2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 31, 40, 40, 31, 15, 31, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 36, 39, 39, 39, 39, 39, 40, 40, 40, 40, 40, 40, 40, 15, 15, 3, 3, 1, 3, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 40, 40] 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: 199 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918082 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523918082 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918082/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918082/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918082 Building ZINC001523918083 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918083' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918083 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523918083 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918083/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918083 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/844 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)N2CCCCC2)cc1) `ZINC001523918083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523918083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523918083 none COc1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)N2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 38, 40, 40, 31, 16, 31, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 36, 39, 39, 39, 39, 39, 40, 40, 40, 40, 40, 40, 40, 16, 16, 3, 3, 1, 3, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 40, 40] 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: 168 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918083 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918083/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918083 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 845) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/845 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/845' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)N2CCCCC2)cc1) `ZINC001523918083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523918083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523918083 none COc1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)N2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 29, 41, 41, 29, 14, 29, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 32, 36, 36, 36, 36, 36, 41, 41, 41, 41, 41, 41, 41, 14, 14, 4, 3, 1, 3, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 41, 41] 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: 203 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918083 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523918083 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918083/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918083/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918083 Building ZINC001523918083 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918083' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918083 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523918083 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918083/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918083 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 844) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)N2CCCCC2)cc1) `ZINC001523918083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523918083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523918083 none COc1ccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)N2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 38, 40, 40, 31, 16, 31, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 36, 39, 39, 39, 39, 39, 40, 40, 40, 40, 40, 40, 40, 16, 16, 3, 3, 1, 3, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 40, 40] 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: 168 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918083 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918083/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918083 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 845) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)N2CCCCC2)cc1) `ZINC001523918083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523918083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523918083 none COc1ccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)N2CCCCC2)cc1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 29, 41, 41, 29, 14, 29, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 32, 36, 36, 36, 36, 36, 41, 41, 41, 41, 41, 41, 41, 14, 14, 4, 3, 1, 3, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 41, 41] 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: 203 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918083 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523918083 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918083/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918083/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918083 Building ZINC001523918843 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918843' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918843 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523918843 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918843/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918843 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/846 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1c(c2ccc(F)cc2)csc1NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC001523918843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523918843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523918843 none CCOC(=O)c1c(c2ccc(F)cc2)csc1NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', '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', '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, 15, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 30, 30, 8, 30, 8, 8, 8, 15, 15, 8, 12, 15, 15, 8, 8, 3, 3, 1, 3, 1, 1, 1, 5, 5, 2, 5, 5, 5, 5, 43, 43, 43, 43, 43, 15, 15, 15, 15, 8, 3, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918843 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918843/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918843 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 847) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/847 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/847' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1c(c2ccc(F)cc2)csc1NC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC001523918843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523918843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523918843 none CCOC(=O)c1c(c2ccc(F)cc2)csc1NC(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', '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', '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, 15, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 29, 29, 8, 29, 8, 8, 8, 15, 15, 8, 8, 15, 15, 8, 8, 3, 3, 1, 3, 1, 1, 1, 5, 5, 2, 5, 5, 5, 5, 42, 42, 42, 42, 42, 15, 15, 15, 15, 8, 3, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918843 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523918843 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918843/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918843/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918843 Building ZINC001523918843 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918843' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918843 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523918843 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918843/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918843 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 846) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOC(=O)c1c(c2ccc(F)cc2)csc1NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC001523918843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523918843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523918843 none CCOC(=O)c1c(c2ccc(F)cc2)csc1NC(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', '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', '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, 15, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 30, 30, 8, 30, 8, 8, 8, 15, 15, 8, 12, 15, 15, 8, 8, 3, 3, 1, 3, 1, 1, 1, 5, 5, 2, 5, 5, 5, 5, 43, 43, 43, 43, 43, 15, 15, 15, 15, 8, 3, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918843 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918843/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918843 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 847) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOC(=O)c1c(c2ccc(F)cc2)csc1NC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC001523918843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523918843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523918843 none CCOC(=O)c1c(c2ccc(F)cc2)csc1NC(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', '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', '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, 15, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 29, 29, 8, 29, 8, 8, 8, 15, 15, 8, 8, 15, 15, 8, 8, 3, 3, 1, 3, 1, 1, 1, 5, 5, 2, 5, 5, 5, 5, 42, 42, 42, 42, 42, 15, 15, 15, 15, 8, 3, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918843 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523918843 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918843/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918843/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523918843 Building ZINC001523928217 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001523928217 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/848 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1) `ZINC001523928217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523928217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001523928217 none CN(CCN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 6, 4, 6, 9, 10, 10, 10, 10, 10, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 16, 20, 23, 23, 23, 23, 23, 16, 16, 16, 12, 12, 12, 12, 9, 9, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 23, 23, 23, 23, 23] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 849) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/849 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/849' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1) `ZINC001523928217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523928217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001523928217 none CN(CCN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 6, 4, 6, 9, 10, 10, 10, 10, 10, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 16, 20, 23, 23, 23, 23, 23, 16, 16, 16, 12, 12, 12, 12, 9, 9, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 23, 23, 23, 23, 23] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 850) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/850 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/850' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1) `ZINC001523928217.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001523928217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001523928217 none CN(CCN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 3, 5, 7, 8, 8, 8, 8, 8, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 14, 19, 24, 24, 21, 24, 24, 14, 14, 14, 9, 9, 9, 9, 7, 7, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 24, 24, 24, 24, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 851) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/851 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/851' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1) `ZINC001523928217.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001523928217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001523928217 none CN(CCN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 3, 5, 7, 8, 8, 8, 8, 8, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 14, 19, 24, 24, 21, 24, 24, 14, 14, 14, 9, 9, 9, 9, 7, 7, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 24, 24, 24, 24, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523928217 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 Building ZINC001523928217 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001523928217 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 848) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CN(CCN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1) `ZINC001523928217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523928217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001523928217 none CN(CCN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 6, 4, 6, 9, 10, 10, 10, 10, 10, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 16, 20, 23, 23, 23, 23, 23, 16, 16, 16, 12, 12, 12, 12, 9, 9, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 23, 23, 23, 23, 23] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 849) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CN(CCN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1) `ZINC001523928217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523928217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001523928217 none CN(CCN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 6, 4, 6, 9, 10, 10, 10, 10, 10, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 16, 20, 23, 23, 23, 23, 23, 16, 16, 16, 12, 12, 12, 12, 9, 9, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 23, 23, 23, 23, 23] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 850) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/850: 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(CCN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1) `ZINC001523928217.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001523928217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001523928217 none CN(CCN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 3, 5, 7, 8, 8, 8, 8, 8, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 14, 19, 24, 24, 21, 24, 24, 14, 14, 14, 9, 9, 9, 9, 7, 7, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 24, 24, 24, 24, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 851) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/851: 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(CCN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1) `ZINC001523928217.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001523928217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001523928217 none CN(CCN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 3, 5, 7, 8, 8, 8, 8, 8, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 14, 19, 24, 24, 21, 24, 24, 14, 14, 14, 9, 9, 9, 9, 7, 7, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 24, 24, 24, 24, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523928217 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 Building ZINC001523928217 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001523928217 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 848) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CN(CCN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1) `ZINC001523928217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523928217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001523928217 none CN(CCN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 6, 4, 6, 9, 10, 10, 10, 10, 10, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 16, 20, 23, 23, 23, 23, 23, 16, 16, 16, 12, 12, 12, 12, 9, 9, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 23, 23, 23, 23, 23] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 849) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CN(CCN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1) `ZINC001523928217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523928217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001523928217 none CN(CCN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 6, 4, 6, 9, 10, 10, 10, 10, 10, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 16, 20, 23, 23, 23, 23, 23, 16, 16, 16, 12, 12, 12, 12, 9, 9, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 23, 23, 23, 23, 23] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 850) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/850: 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(CCN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1) `ZINC001523928217.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001523928217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001523928217 none CN(CCN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 3, 5, 7, 8, 8, 8, 8, 8, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 14, 19, 24, 24, 21, 24, 24, 14, 14, 14, 9, 9, 9, 9, 7, 7, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 24, 24, 24, 24, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 851) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/851: 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(CCN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1) `ZINC001523928217.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001523928217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001523928217 none CN(CCN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 3, 5, 7, 8, 8, 8, 8, 8, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 14, 19, 24, 24, 21, 24, 24, 14, 14, 14, 9, 9, 9, 9, 7, 7, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 24, 24, 24, 24, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523928217 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 Building ZINC001523928217 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001523928217 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 848) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CN(CCN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1) `ZINC001523928217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523928217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001523928217 none CN(CCN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 6, 4, 6, 9, 10, 10, 10, 10, 10, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 16, 20, 23, 23, 23, 23, 23, 16, 16, 16, 12, 12, 12, 12, 9, 9, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 23, 23, 23, 23, 23] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 849) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CN(CCN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1) `ZINC001523928217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523928217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001523928217 none CN(CCN(Cc1ccccc1)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 6, 4, 6, 9, 10, 10, 10, 10, 10, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 16, 20, 23, 23, 23, 23, 23, 16, 16, 16, 12, 12, 12, 12, 9, 9, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 23, 23, 23, 23, 23] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 850) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/850: 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(CCN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1) `ZINC001523928217.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001523928217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001523928217 none CN(CCN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 3, 5, 7, 8, 8, 8, 8, 8, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 14, 19, 24, 24, 21, 24, 24, 14, 14, 14, 9, 9, 9, 9, 7, 7, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 24, 24, 24, 24, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 851) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/851: 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(CCN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1) `ZINC001523928217.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001523928217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001523928217 none CN(CCN(Cc1ccccc1)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 3, 5, 7, 8, 8, 8, 8, 8, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 14, 19, 24, 24, 21, 24, 24, 14, 14, 14, 9, 9, 9, 9, 7, 7, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 24, 24, 24, 24, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523928217 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523928217 Building ZINC001523970865 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523970865' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523970865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523970865 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523970865/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523970865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/852 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(CCC2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)CC2)cc1) `ZINC001523970865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523970865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523970865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523970865 none CCOc1ccc(CCC2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 6, 12, 12, 6, 6, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 3, 3, 2, 3, 6, 3, 3, 3, 3, 3, 12, 12, 24, 24, 24, 24, 24, 12, 12, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 3, 3, 3, 3, 3, 12, 12] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523970865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523970865/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523970865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 853) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/853 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/853' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(CCC2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)CC2)cc1) `ZINC001523970865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523970865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523970865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523970865 none CCOc1ccc(CCC2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 7, 13, 13, 7, 7, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 2, 2, 2, 2, 4, 2, 2, 2, 3, 3, 13, 13, 25, 25, 25, 25, 25, 13, 13, 7, 7, 7, 7, 3, 3, 3, 3, 3, 2, 2, 4, 4, 4, 2, 3, 3, 3, 3, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523970865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523970865 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523970865/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523970865/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523970865 Building ZINC001523970865 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523970865' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523970865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523970865 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523970865/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523970865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 852) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOc1ccc(CCC2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)CC2)cc1) `ZINC001523970865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523970865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523970865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523970865 none CCOc1ccc(CCC2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 6, 12, 12, 6, 6, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 3, 3, 2, 3, 6, 3, 3, 3, 3, 3, 12, 12, 24, 24, 24, 24, 24, 12, 12, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 3, 3, 3, 3, 3, 12, 12] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523970865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523970865/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523970865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 853) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOc1ccc(CCC2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)CC2)cc1) `ZINC001523970865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523970865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523970865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001523970865 none CCOc1ccc(CCC2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(OC)c(Cl)c3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 7, 13, 13, 7, 7, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 2, 2, 2, 2, 4, 2, 2, 2, 3, 3, 13, 13, 25, 25, 25, 25, 25, 13, 13, 7, 7, 7, 7, 3, 3, 3, 3, 3, 2, 2, 4, 4, 4, 2, 3, 3, 3, 3, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523970865 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523970865 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523970865/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523970865/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523970865 Building ZINC001523976038 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976038' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976038 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523976038 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976038/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976038 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/854 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](Cc1ccccc1)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001523976038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523976038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001523976038 none O=C(NC[C@H](Cc1ccccc1)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', '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', '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, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 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, 36, 34, 39, 39, 39, 39, 39, 39, 36, 36, 36, 36, 36, 36, 1, 1, 1, 7, 7, 7, 7, 7, 3, 16, 16, 39, 39, 39, 39, 39, 39, 39, 36, 36, 36, 36, 36, 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, 40, 41, 42, 43]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976038 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976038/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976038 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 855) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/855 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/855' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](Cc1ccccc1)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001523976038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523976038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001523976038 none O=C(NC[C@H](Cc1ccccc1)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', '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', '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, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 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, 33, 32, 35, 35, 35, 35, 35, 35, 33, 34, 34, 33, 34, 34, 1, 1, 1, 7, 7, 7, 7, 7, 3, 17, 17, 35, 35, 35, 35, 35, 35, 35, 34, 34, 33, 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, 40, 41, 42, 43]) total number of confs: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976038 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523976038 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976038/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976038/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976038 Building ZINC001523976038 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976038' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976038 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523976038 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976038/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976038 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 854) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NC[C@H](Cc1ccccc1)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001523976038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523976038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001523976038 none O=C(NC[C@H](Cc1ccccc1)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', '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', '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, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 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, 36, 34, 39, 39, 39, 39, 39, 39, 36, 36, 36, 36, 36, 36, 1, 1, 1, 7, 7, 7, 7, 7, 3, 16, 16, 39, 39, 39, 39, 39, 39, 39, 36, 36, 36, 36, 36, 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, 40, 41, 42, 43]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976038 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976038/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976038 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 855) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NC[C@H](Cc1ccccc1)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001523976038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523976038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001523976038 none O=C(NC[C@H](Cc1ccccc1)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', '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', '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, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 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, 33, 32, 35, 35, 35, 35, 35, 35, 33, 34, 34, 33, 34, 34, 1, 1, 1, 7, 7, 7, 7, 7, 3, 17, 17, 35, 35, 35, 35, 35, 35, 35, 34, 34, 33, 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, 40, 41, 42, 43]) total number of confs: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976038 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523976038 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976038/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976038/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976038 Building ZINC001523976039 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976039' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976039 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523976039 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976039/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976039 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/856 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](Cc1ccccc1)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001523976039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523976039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001523976039 none O=C(NC[C@@H](Cc1ccccc1)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', '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', '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, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 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, 34, 33, 36, 36, 36, 36, 36, 36, 34, 35, 35, 34, 35, 35, 1, 1, 1, 7, 7, 7, 7, 7, 3, 17, 17, 36, 36, 36, 36, 36, 36, 36, 35, 35, 34, 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, 40, 41, 42, 43]) total number of confs: 168 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976039 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976039/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976039 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 857) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/857 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/857' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](Cc1ccccc1)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001523976039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523976039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001523976039 none O=C(NC[C@@H](Cc1ccccc1)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', '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', '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, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 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, 35, 33, 39, 39, 39, 39, 39, 39, 35, 35, 35, 35, 35, 35, 1, 1, 1, 7, 7, 7, 7, 7, 3, 16, 16, 39, 39, 39, 39, 39, 39, 39, 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, 40, 41, 42, 43]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976039 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523976039 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976039/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976039/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976039 Building ZINC001523976039 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976039' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976039 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001523976039 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976039/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976039 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 856) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NC[C@@H](Cc1ccccc1)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001523976039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001523976039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001523976039 none O=C(NC[C@@H](Cc1ccccc1)c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', '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', '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, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 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, 34, 33, 36, 36, 36, 36, 36, 36, 34, 35, 35, 34, 35, 35, 1, 1, 1, 7, 7, 7, 7, 7, 3, 17, 17, 36, 36, 36, 36, 36, 36, 36, 35, 35, 34, 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, 40, 41, 42, 43]) total number of confs: 168 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976039 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976039/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976039 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 857) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NC[C@@H](Cc1ccccc1)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001523976039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001523976039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001523976039 none O=C(NC[C@@H](Cc1ccccc1)c1ccccc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', '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', '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, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 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, 35, 33, 39, 39, 39, 39, 39, 39, 35, 35, 35, 35, 35, 35, 1, 1, 1, 7, 7, 7, 7, 7, 3, 16, 16, 39, 39, 39, 39, 39, 39, 39, 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, 40, 41, 42, 43]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976039 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001523976039 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976039/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976039/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001523976039 Building ZINC001524033683 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524033683' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524033683 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524033683 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524033683/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524033683 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/858 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cn(Cc2ccccc2)nc1c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001524033683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524033683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524033683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001524033683 none O=C(NCc1cn(Cc2ccccc2)nc1c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 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, 26, 26, 26, 49, 50, 50, 50, 50, 50, 26, 26, 26, 27, 27, 26, 27, 27, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 8, 8, 26, 49, 49, 50, 50, 50, 50, 50, 27, 27, 26, 27, 27, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524033683 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524033683/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524033683 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 859) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/859 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/859' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cn(Cc2ccccc2)nc1c1ccccc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001524033683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524033683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524033683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001524033683 none O=C(NCc1cn(Cc2ccccc2)nc1c1ccccc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 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, 27, 27, 27, 49, 50, 50, 49, 50, 50, 27, 27, 27, 28, 28, 28, 28, 28, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 9, 9, 27, 49, 49, 50, 50, 50, 50, 50, 28, 28, 28, 28, 28, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524033683 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524033683 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524033683/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524033683/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524033683 Building ZINC001524033683 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524033683' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524033683 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524033683 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524033683/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524033683 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 858) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NCc1cn(Cc2ccccc2)nc1c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001524033683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524033683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524033683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001524033683 none O=C(NCc1cn(Cc2ccccc2)nc1c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 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, 26, 26, 26, 49, 50, 50, 50, 50, 50, 26, 26, 26, 27, 27, 26, 27, 27, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 8, 8, 26, 49, 49, 50, 50, 50, 50, 50, 27, 27, 26, 27, 27, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524033683 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524033683/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524033683 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 859) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(NCc1cn(Cc2ccccc2)nc1c1ccccc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001524033683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524033683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524033683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001524033683 none O=C(NCc1cn(Cc2ccccc2)nc1c1ccccc1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 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, 27, 27, 27, 49, 50, 50, 49, 50, 50, 27, 27, 27, 28, 28, 28, 28, 28, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 9, 9, 27, 49, 49, 50, 50, 50, 50, 50, 28, 28, 28, 28, 28, 2, 2, 2, 2] 50 rigid atoms, others: [1, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524033683 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524033683 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524033683/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524033683/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524033683 Building ZINC001524035598 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524035598' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524035598 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524035598 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524035598/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524035598 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/860 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cn(Cc2ccccc2)nc1c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001524035598.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524035598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524035598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001524035598 none O=C(NCc1cn(Cc2ccccc2)nc1c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 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, 7, 7, 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] 0 hydrogens need rotated 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, 27, 27, 27, 48, 49, 49, 49, 49, 49, 27, 27, 27, 28, 28, 27, 28, 28, 1, 1, 1, 3, 3, 3, 3, 3, 2, 10, 10, 27, 48, 48, 49, 49, 49, 49, 49, 28, 28, 28, 28, 28, 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, 47]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524035598 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524035598/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524035598 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 861) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/861 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/861' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cn(Cc2ccccc2)nc1c1ccccc1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001524035598.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524035598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524035598/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001524035598 none O=C(NCc1cn(Cc2ccccc2)nc1c1ccccc1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 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, 7, 7, 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] 0 hydrogens need rotated 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, 27, 27, 27, 48, 49, 49, 48, 49, 49, 27, 27, 27, 28, 28, 28, 28, 28, 1, 1, 1, 3, 3, 3, 3, 3, 2, 10, 10, 27, 48, 48, 49, 49, 49, 49, 49, 28, 28, 28, 28, 28, 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, 47]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524035598 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524035598 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524035598/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524035598/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524035598 Building ZINC001524035598 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524035598' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524035598 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524035598 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524035598/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524035598 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 860) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(NCc1cn(Cc2ccccc2)nc1c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001524035598.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524035598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524035598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001524035598 none O=C(NCc1cn(Cc2ccccc2)nc1c1ccccc1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 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, 7, 7, 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] 0 hydrogens need rotated 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, 27, 27, 27, 48, 49, 49, 49, 49, 49, 27, 27, 27, 28, 28, 27, 28, 28, 1, 1, 1, 3, 3, 3, 3, 3, 2, 10, 10, 27, 48, 48, 49, 49, 49, 49, 49, 28, 28, 28, 28, 28, 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, 47]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524035598 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524035598/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524035598 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 861) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(NCc1cn(Cc2ccccc2)nc1c1ccccc1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001524035598.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524035598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524035598/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001524035598 none O=C(NCc1cn(Cc2ccccc2)nc1c1ccccc1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 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, 7, 7, 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] 0 hydrogens need rotated 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, 27, 27, 27, 48, 49, 49, 48, 49, 49, 27, 27, 27, 28, 28, 28, 28, 28, 1, 1, 1, 3, 3, 3, 3, 3, 2, 10, 10, 27, 48, 48, 49, 49, 49, 49, 49, 28, 28, 28, 28, 28, 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, 47]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524035598 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524035598 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524035598/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524035598/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524035598 Building ZINC001524040862 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524040862' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524040862 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524040862 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524040862/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524040862 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/862 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSc1cccc(Br)c1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001524040862.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524040862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524040862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001524040862 none CCSc1cccc(Br)c1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 5, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 32, 32, 32, 32, 32, 10, 10, 10, 3, 7, 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524040862 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524040862/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524040862 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 863) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/863 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/863' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSc1cccc(Br)c1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001524040862.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524040862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524040862/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001524040862 none CCSc1cccc(Br)c1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 10, 10, 10, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 34, 34, 34, 34, 34, 10, 10, 10, 3, 7, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524040862 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524040862 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524040862/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524040862/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524040862 Building ZINC001524040862 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524040862' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524040862 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524040862 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524040862/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524040862 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 862) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCSc1cccc(Br)c1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001524040862.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524040862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524040862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001524040862 none CCSc1cccc(Br)c1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 5, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 32, 32, 32, 32, 32, 10, 10, 10, 3, 7, 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524040862 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524040862/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524040862 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 863) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCSc1cccc(Br)c1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001524040862.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524040862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524040862/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001524040862 none CCSc1cccc(Br)c1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 17, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 10, 10, 10, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 34, 34, 34, 34, 34, 10, 10, 10, 3, 7, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524040862 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524040862 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524040862/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524040862/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524040862 Building ZINC001524055168 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524055168' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524055168 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524055168 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524055168/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524055168 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/864 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(c2c(Cl)cccc2Cl)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001524055168.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524055168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524055168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001524055168 none O=C(N1CCC(c2c(Cl)cccc2Cl)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 16, 1, 1, 1, 1, 16, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 10, 10, 10, 10, 17, 17, 10, 17, 17, 10, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 10, 17, 17, 12, 17, 17, 10] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524055168 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524055168/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524055168 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 865) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/865 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/865' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(c2c(Cl)cccc2Cl)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001524055168.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524055168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524055168/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001524055168 none O=C(N1CCC(c2c(Cl)cccc2Cl)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 16, 1, 1, 1, 1, 16, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 10, 10, 10, 10, 19, 19, 10, 19, 19, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10, 19, 19, 10, 19, 19, 10] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524055168 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524055168 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524055168/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524055168/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524055168 Building ZINC001524055168 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524055168' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524055168 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524055168 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524055168/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524055168 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 864) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CCC(c2c(Cl)cccc2Cl)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001524055168.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524055168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524055168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001524055168 none O=C(N1CCC(c2c(Cl)cccc2Cl)CC1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 16, 1, 1, 1, 1, 16, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 10, 10, 10, 10, 17, 17, 10, 17, 17, 10, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 10, 17, 17, 12, 17, 17, 10] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524055168 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524055168/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524055168 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 865) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CCC(c2c(Cl)cccc2Cl)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001524055168.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524055168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524055168/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001524055168 none O=C(N1CCC(c2c(Cl)cccc2Cl)CC1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 16, 1, 1, 1, 1, 16, 5, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 10, 10, 10, 10, 19, 19, 10, 19, 19, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10, 19, 19, 10, 19, 19, 10] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524055168 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524055168 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524055168/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524055168/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524055168 Building ZINC001524064994 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524064994' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524064994 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524064994 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524064994/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524064994 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/866 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Cc1cccc(F)c1)c1cc(Cl)cnc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001524064994.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524064994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524064994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524064994 none O=C(Cc1cccc(F)c1)c1cc(Cl)cnc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 29, 29, 29, 29, 29, 29, 6, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 29, 29, 29, 29, 6, 6, 2, 4, 4, 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524064994 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524064994/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524064994 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 867) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/867 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/867' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Cc1cccc(F)c1)c1cc(Cl)cnc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001524064994.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524064994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524064994/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524064994 none O=C(Cc1cccc(F)c1)c1cc(Cl)cnc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 30, 30, 30, 30, 6, 6, 2, 4, 4, 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524064994 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524064994 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524064994/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524064994/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524064994 Building ZINC001524064994 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524064994' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524064994 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524064994 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524064994/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524064994 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 866) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Cc1cccc(F)c1)c1cc(Cl)cnc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001524064994.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524064994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524064994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524064994 none O=C(Cc1cccc(F)c1)c1cc(Cl)cnc1NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 29, 29, 29, 29, 29, 29, 6, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 29, 29, 29, 29, 6, 6, 2, 4, 4, 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524064994 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524064994/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524064994 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 867) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Cc1cccc(F)c1)c1cc(Cl)cnc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001524064994.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524064994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524064994/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524064994 none O=C(Cc1cccc(F)c1)c1cc(Cl)cnc1NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 16, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 30, 30, 30, 30, 6, 6, 2, 4, 4, 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524064994 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524064994 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524064994/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524064994/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524064994 Building ZINC001524094999 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524094999' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524094999 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524094999 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524094999/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524094999 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/868 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC(C)(C)Oc3ccc(NC(=O)OC(C)(C)C)cc32)cc1) `ZINC001524094999.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524094999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524094999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001524094999 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC(C)(C)Oc3ccc(NC(=O)OC(C)(C)C)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 31, 42, 42, 50, 50, 50, 50, 6, 6, 2, 2, 2, 2, 2, 2, 2, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524094999 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524094999/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524094999 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 869) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/869 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/869' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC(C)(C)Oc3ccc(NC(=O)OC(C)(C)C)cc32)cc1) `ZINC001524094999.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524094999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524094999/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001524094999 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC(C)(C)Oc3ccc(NC(=O)OC(C)(C)C)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 32, 44, 44, 50, 50, 50, 50, 8, 8, 2, 2, 2, 2, 2, 2, 2, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524094999 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524094999 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524094999/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524094999/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524094999 Building ZINC001524094999 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524094999' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524094999 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524094999 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524094999/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524094999 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 868) grep: /scratch/xiaobo/12845/xbi-8058088.35/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([C@@]([O-])([SiH3])C(=O)N[C@H]2CC(C)(C)Oc3ccc(NC(=O)OC(C)(C)C)cc32)cc1) `ZINC001524094999.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524094999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524094999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001524094999 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC(C)(C)Oc3ccc(NC(=O)OC(C)(C)C)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 31, 42, 42, 50, 50, 50, 50, 6, 6, 2, 2, 2, 2, 2, 2, 2, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524094999 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524094999/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524094999 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 869) grep: /scratch/xiaobo/12845/xbi-8058088.35/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([C@]([O-])([SiH3])C(=O)N[C@H]2CC(C)(C)Oc3ccc(NC(=O)OC(C)(C)C)cc32)cc1) `ZINC001524094999.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524094999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524094999/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001524094999 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC(C)(C)Oc3ccc(NC(=O)OC(C)(C)C)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 32, 44, 44, 50, 50, 50, 50, 8, 8, 2, 2, 2, 2, 2, 2, 2, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524094999 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524094999 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524094999/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524094999/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524094999 Building ZINC001524095003 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524095003' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524095003 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524095003 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524095003/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524095003 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/870 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC(C)(C)Oc3ccc(NC(=O)OC(C)(C)C)cc32)cc1) `ZINC001524095003.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524095003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524095003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001524095003 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC(C)(C)Oc3ccc(NC(=O)OC(C)(C)C)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 29, 42, 42, 50, 50, 50, 50, 8, 8, 2, 2, 2, 2, 2, 2, 2, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524095003 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524095003/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524095003 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 871) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/871 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/871' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC(C)(C)Oc3ccc(NC(=O)OC(C)(C)C)cc32)cc1) `ZINC001524095003.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524095003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524095003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001524095003 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC(C)(C)Oc3ccc(NC(=O)OC(C)(C)C)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 33, 44, 44, 50, 50, 50, 50, 6, 6, 2, 2, 2, 2, 2, 2, 2, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524095003 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524095003 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524095003/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524095003/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524095003 Building ZINC001524095003 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524095003' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524095003 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524095003 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524095003/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524095003 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 870) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/870: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC(C)(C)Oc3ccc(NC(=O)OC(C)(C)C)cc32)cc1) `ZINC001524095003.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524095003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524095003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001524095003 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC(C)(C)Oc3ccc(NC(=O)OC(C)(C)C)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 29, 42, 42, 50, 50, 50, 50, 8, 8, 2, 2, 2, 2, 2, 2, 2, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524095003 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524095003/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524095003 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 871) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/871: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC(C)(C)Oc3ccc(NC(=O)OC(C)(C)C)cc32)cc1) `ZINC001524095003.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524095003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524095003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001524095003 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC(C)(C)Oc3ccc(NC(=O)OC(C)(C)C)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 33, 44, 44, 50, 50, 50, 50, 6, 6, 2, 2, 2, 2, 2, 2, 2, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524095003 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524095003 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524095003/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524095003/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524095003 Building ZINC001524165576 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001524165576 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/872 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](c2ccc(Cl)cc2NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001524165576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524165576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001524165576 none CC[N@]1CC[N@](c2ccc(Cl)cc2NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 39, 36, 14, 10, 10, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 39, 39, 40, 40, 40, 40, 40, 39, 39, 39, 39, 10, 10, 10, 4, 3, 1, 3, 39, 39, 39, 39] 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, 44, 45, 46, 47]) total number of confs: 88 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 873) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/873 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/873' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](c2ccc(Cl)cc2NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001524165576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524165576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001524165576 none CC[N@]1CC[N@@](c2ccc(Cl)cc2NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 39, 37, 16, 11, 11, 6, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 39, 39, 40, 40, 40, 40, 40, 39, 39, 39, 39, 11, 11, 11, 4, 3, 1, 3, 39, 39, 39, 39] 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, 44, 45, 46, 47]) total number of confs: 108 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 874) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/874 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/874' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](c2ccc(Cl)cc2NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001524165576.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001524165576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001524165576 none CC[N@]1CC[N@](c2ccc(Cl)cc2NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 41, 41, 17, 11, 11, 7, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 11, 11, 11, 4, 3, 1, 3, 41, 41, 41, 41] 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, 44, 45, 46, 47]) total number of confs: 89 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 875) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/875 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/875' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](c2ccc(Cl)cc2NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001524165576.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001524165576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001524165576 none CC[N@]1CC[N@@](c2ccc(Cl)cc2NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 17, 11, 11, 4, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 11, 11, 11, 4, 3, 3, 3, 40, 40, 40, 40] 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]) total number of confs: 95 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524165576 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 Building ZINC001524165576 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001524165576 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 872) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC[N@]1CC[N@](c2ccc(Cl)cc2NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001524165576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524165576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001524165576 none CC[N@]1CC[N@](c2ccc(Cl)cc2NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 39, 36, 14, 10, 10, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 39, 39, 40, 40, 40, 40, 40, 39, 39, 39, 39, 10, 10, 10, 4, 3, 1, 3, 39, 39, 39, 39] 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, 44, 45, 46, 47]) total number of confs: 88 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 873) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC[N@]1CC[N@@](c2ccc(Cl)cc2NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001524165576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524165576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001524165576 none CC[N@]1CC[N@@](c2ccc(Cl)cc2NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 39, 37, 16, 11, 11, 6, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 39, 39, 40, 40, 40, 40, 40, 39, 39, 39, 39, 11, 11, 11, 4, 3, 1, 3, 39, 39, 39, 39] 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, 44, 45, 46, 47]) total number of confs: 108 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 874) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/874: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](c2ccc(Cl)cc2NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001524165576.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001524165576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001524165576 none CC[N@]1CC[N@](c2ccc(Cl)cc2NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 41, 41, 17, 11, 11, 7, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 11, 11, 11, 4, 3, 1, 3, 41, 41, 41, 41] 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, 44, 45, 46, 47]) total number of confs: 89 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 875) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/875: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](c2ccc(Cl)cc2NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001524165576.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001524165576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001524165576 none CC[N@]1CC[N@@](c2ccc(Cl)cc2NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 17, 11, 11, 4, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 11, 11, 11, 4, 3, 3, 3, 40, 40, 40, 40] 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]) total number of confs: 95 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524165576 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 Building ZINC001524165576 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001524165576 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 872) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC[N@]1CC[N@](c2ccc(Cl)cc2NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001524165576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524165576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001524165576 none CC[N@]1CC[N@](c2ccc(Cl)cc2NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 39, 36, 14, 10, 10, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 39, 39, 40, 40, 40, 40, 40, 39, 39, 39, 39, 10, 10, 10, 4, 3, 1, 3, 39, 39, 39, 39] 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, 44, 45, 46, 47]) total number of confs: 88 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 873) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC[N@]1CC[N@@](c2ccc(Cl)cc2NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001524165576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524165576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001524165576 none CC[N@]1CC[N@@](c2ccc(Cl)cc2NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 39, 37, 16, 11, 11, 6, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 39, 39, 40, 40, 40, 40, 40, 39, 39, 39, 39, 11, 11, 11, 4, 3, 1, 3, 39, 39, 39, 39] 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, 44, 45, 46, 47]) total number of confs: 108 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 874) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/874: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](c2ccc(Cl)cc2NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001524165576.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001524165576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001524165576 none CC[N@]1CC[N@](c2ccc(Cl)cc2NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 41, 41, 17, 11, 11, 7, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 11, 11, 11, 4, 3, 1, 3, 41, 41, 41, 41] 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, 44, 45, 46, 47]) total number of confs: 89 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 875) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/875: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](c2ccc(Cl)cc2NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001524165576.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001524165576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001524165576 none CC[N@]1CC[N@@](c2ccc(Cl)cc2NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 17, 11, 11, 4, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 11, 11, 11, 4, 3, 3, 3, 40, 40, 40, 40] 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]) total number of confs: 95 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524165576 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 Building ZINC001524165576 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001524165576 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 872) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC[N@]1CC[N@](c2ccc(Cl)cc2NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001524165576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524165576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001524165576 none CC[N@]1CC[N@](c2ccc(Cl)cc2NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 39, 36, 14, 10, 10, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 39, 39, 40, 40, 40, 40, 40, 39, 39, 39, 39, 10, 10, 10, 4, 3, 1, 3, 39, 39, 39, 39] 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, 44, 45, 46, 47]) total number of confs: 88 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 873) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC[N@]1CC[N@@](c2ccc(Cl)cc2NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001524165576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524165576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001524165576 none CC[N@]1CC[N@@](c2ccc(Cl)cc2NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 39, 37, 16, 11, 11, 6, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 39, 39, 40, 40, 40, 40, 40, 39, 39, 39, 39, 11, 11, 11, 4, 3, 1, 3, 39, 39, 39, 39] 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, 44, 45, 46, 47]) total number of confs: 108 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 874) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/874: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](c2ccc(Cl)cc2NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001524165576.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001524165576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001524165576 none CC[N@]1CC[N@](c2ccc(Cl)cc2NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 41, 41, 17, 11, 11, 7, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 11, 11, 11, 4, 3, 1, 3, 41, 41, 41, 41] 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, 44, 45, 46, 47]) total number of confs: 89 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 875) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/875: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](c2ccc(Cl)cc2NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001524165576.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001524165576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001524165576 none CC[N@]1CC[N@@](c2ccc(Cl)cc2NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 17, 11, 11, 4, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 11, 11, 11, 4, 3, 3, 3, 40, 40, 40, 40] 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]) total number of confs: 95 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524165576 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524165576 Building ZINC001524172113 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524172113' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524172113 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524172113 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524172113/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524172113 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/876 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001524172113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524172113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524172113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001524172113 none O=C(Nc1ccccc1)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 0 hydrogens 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, 34, 34, 20, 34, 34, 2, 2, 10, 10, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 10, 10, 19, 34, 34, 34, 34, 34, 19, 10, 10, 2, 7, 7, 10, 10] 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]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524172113 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524172113/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524172113 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 877) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/877 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/877' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001524172113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524172113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524172113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001524172113 none O=C(Nc1ccccc1)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 0 hydrogens 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, 38, 38, 36, 38, 38, 8, 2, 11, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 21, 38, 38, 38, 38, 38, 21, 11, 11, 2, 6, 6, 11, 11] 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524172113 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524172113 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524172113/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524172113/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524172113 Building ZINC001524172113 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524172113' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524172113 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524172113 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524172113/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524172113 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 876) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ccccc1)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001524172113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524172113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524172113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001524172113 none O=C(Nc1ccccc1)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 0 hydrogens 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, 34, 34, 20, 34, 34, 2, 2, 10, 10, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 10, 10, 19, 34, 34, 34, 34, 34, 19, 10, 10, 2, 7, 7, 10, 10] 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]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524172113 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524172113/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524172113 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 877) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ccccc1)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1) `ZINC001524172113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524172113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524172113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001524172113 none O=C(Nc1ccccc1)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 0 hydrogens 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, 38, 38, 36, 38, 38, 8, 2, 11, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 21, 38, 38, 38, 38, 38, 21, 11, 11, 2, 6, 6, 11, 11] 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524172113 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524172113 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524172113/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524172113/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524172113 Building ZINC001524178204 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524178204' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524178204 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524178204 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524178204/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524178204 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/878 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Sc3nc(C)cc(C)n3)cc2)cc1Cl) `ZINC001524178204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524178204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524178204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001524178204 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Sc3nc(C)cc(C)n3)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', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 8, 1, 5, 1, 1, 5, 8, 1, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 11, 29, 29, 29, 11, 29, 29, 29, 2, 2, 2, 2, 2, 4, 4, 4, 2, 2, 1, 2, 2, 29, 29, 29, 11, 29, 29, 29, 2, 2, 2] 50 rigid atoms, others: [34, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524178204 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524178204/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524178204 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 879) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/879 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/879' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Sc3nc(C)cc(C)n3)cc2)cc1Cl) `ZINC001524178204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524178204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524178204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001524178204 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Sc3nc(C)cc(C)n3)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', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 8, 1, 5, 1, 1, 5, 8, 1, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 12, 30, 30, 30, 18, 30, 30, 30, 2, 2, 2, 2, 2, 4, 4, 4, 2, 2, 1, 2, 2, 30, 30, 30, 18, 30, 30, 30, 2, 2, 2] 50 rigid atoms, others: [34, 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, 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/12845/xbi-8058088.35/working/building/ZINC001524178204 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524178204 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524178204/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524178204/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524178204 Building ZINC001524178204 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524178204' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524178204 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524178204 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524178204/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524178204 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 878) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Sc3nc(C)cc(C)n3)cc2)cc1Cl) `ZINC001524178204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524178204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524178204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001524178204 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Sc3nc(C)cc(C)n3)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', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 8, 1, 5, 1, 1, 5, 8, 1, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 11, 29, 29, 29, 11, 29, 29, 29, 2, 2, 2, 2, 2, 4, 4, 4, 2, 2, 1, 2, 2, 29, 29, 29, 11, 29, 29, 29, 2, 2, 2] 50 rigid atoms, others: [34, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524178204 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524178204/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524178204 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 879) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Sc3nc(C)cc(C)n3)cc2)cc1Cl) `ZINC001524178204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524178204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524178204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001524178204 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Sc3nc(C)cc(C)n3)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', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 8, 1, 5, 1, 1, 5, 8, 1, 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, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 12, 30, 30, 30, 18, 30, 30, 30, 2, 2, 2, 2, 2, 4, 4, 4, 2, 2, 1, 2, 2, 30, 30, 30, 18, 30, 30, 30, 2, 2, 2] 50 rigid atoms, others: [34, 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, 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/12845/xbi-8058088.35/working/building/ZINC001524178204 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524178204 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524178204/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524178204/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524178204 Building ZINC001524187753 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187753' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524187753 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187753/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/880 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/880' -> `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])c1ccc(Cl)s1) `ZINC001524187753.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524187753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001524187753 none C[C@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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.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: [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, 16, 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, 7, 7, 7, 7, 7, 9, 6, 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 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 9, 12, 25, 25, 23, 23, 25, 25, 25, 25, 25, 12, 12, 12, 12, 8, 2, 8, 1, 1, 1, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12, 25, 25, 25, 25, 12, 12, 12, 12, 12, 10, 10] 39 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]) total number of confs: 92 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187753/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 881) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/881 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/881' -> `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])c1ccc(Cl)s1) `ZINC001524187753.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524187753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187753/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001524187753 none C[C@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 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.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: [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, 16, 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, 7, 7, 7, 7, 7, 9, 6, 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, 24, 24, 16, 16, 24, 24, 24, 24, 24, 9, 9, 9, 9, 7, 2, 7, 1, 1, 1, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 24, 24, 24, 24, 9, 9, 9, 9, 9, 8, 8] 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]) total number of confs: 100 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524187753 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187753/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187753/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187753 Building ZINC001524187753 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187753' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524187753 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187753/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 880) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001524187753.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524187753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001524187753 none C[C@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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.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: [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, 16, 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, 7, 7, 7, 7, 7, 9, 6, 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 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 9, 12, 25, 25, 23, 23, 25, 25, 25, 25, 25, 12, 12, 12, 12, 8, 2, 8, 1, 1, 1, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12, 25, 25, 25, 25, 12, 12, 12, 12, 12, 10, 10] 39 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]) total number of confs: 92 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187753/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 881) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001524187753.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524187753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187753/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001524187753 none C[C@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 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.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: [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, 16, 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, 7, 7, 7, 7, 7, 9, 6, 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, 24, 24, 16, 16, 24, 24, 24, 24, 24, 9, 9, 9, 9, 7, 2, 7, 1, 1, 1, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 24, 24, 24, 24, 9, 9, 9, 9, 9, 8, 8] 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]) total number of confs: 100 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524187753 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187753/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187753/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187753 Building ZINC001524187754 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187754' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187754 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524187754 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187754/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187754 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/882 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/882' -> `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])c1ccc(Cl)s1) `ZINC001524187754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524187754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001524187754 none C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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.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: [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, 16, 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, 7, 7, 7, 7, 7, 9, 6, 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: [17, 17, 17, 17, 17, 17, 31, 31, 27, 31, 31, 31, 31, 31, 31, 17, 17, 17, 17, 9, 1, 14, 1, 1, 1, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 31, 31, 31, 31, 17, 17, 17, 17, 17, 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187754 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187754/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187754 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 883) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/883 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/883' -> `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])c1ccc(Cl)s1) `ZINC001524187754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524187754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001524187754 none C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 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.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: [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, 16, 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, 7, 7, 7, 7, 7, 9, 6, 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: [14, 14, 14, 14, 14, 14, 27, 27, 23, 27, 27, 27, 27, 27, 27, 14, 14, 14, 14, 6, 1, 10, 1, 1, 1, 7, 7, 7, 7, 7, 14, 14, 14, 14, 14, 27, 27, 27, 27, 14, 14, 14, 14, 14, 7, 7] 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]) total number of confs: 76 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187754 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524187754 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187754/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187754/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187754 Building ZINC001524187754 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187754' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187754 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524187754 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187754/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187754 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 882) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001524187754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524187754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001524187754 none C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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.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: [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, 16, 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, 7, 7, 7, 7, 7, 9, 6, 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: [17, 17, 17, 17, 17, 17, 31, 31, 27, 31, 31, 31, 31, 31, 31, 17, 17, 17, 17, 9, 1, 14, 1, 1, 1, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 31, 31, 31, 31, 17, 17, 17, 17, 17, 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187754 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187754/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187754 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 883) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001524187754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524187754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001524187754 none C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 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.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: [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, 16, 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, 7, 7, 7, 7, 7, 9, 6, 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: [14, 14, 14, 14, 14, 14, 27, 27, 23, 27, 27, 27, 27, 27, 27, 14, 14, 14, 14, 6, 1, 10, 1, 1, 1, 7, 7, 7, 7, 7, 14, 14, 14, 14, 14, 27, 27, 27, 27, 14, 14, 14, 14, 14, 7, 7] 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]) total number of confs: 76 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187754 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524187754 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187754/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187754/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187754 Building ZINC001524187756 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187756' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187756 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524187756 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187756/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187756 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/884 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/884' -> `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])c1ccc(Cl)s1) `ZINC001524187756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524187756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001524187756 none C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@@H](C)N1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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.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: [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, 16, 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, 7, 7, 7, 7, 7, 9, 6, 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, 10, 10, 10, 24, 24, 19, 23, 24, 24, 24, 24, 24, 10, 10, 10, 10, 8, 2, 8, 1, 1, 1, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 24, 24, 24, 24, 10, 10, 10, 10, 10, 9, 9] 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]) total number of confs: 84 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187756 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187756/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187756 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 885) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/885 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/885' -> `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])c1ccc(Cl)s1) `ZINC001524187756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524187756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001524187756 none C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@@H](C)N1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 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.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: [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, 16, 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, 7, 7, 7, 7, 7, 9, 6, 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 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 9, 12, 26, 26, 12, 21, 26, 26, 26, 26, 26, 12, 12, 12, 12, 7, 2, 7, 1, 1, 1, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12, 26, 26, 26, 26, 12, 12, 12, 12, 12, 10, 10] 39 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]) total number of confs: 162 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187756 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524187756 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187756/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187756/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187756 Building ZINC001524187756 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187756' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187756 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524187756 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187756/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187756 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 884) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@@H](C)N1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001524187756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524187756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001524187756 none C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@@H](C)N1C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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.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: [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, 16, 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, 7, 7, 7, 7, 7, 9, 6, 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, 10, 10, 10, 24, 24, 19, 23, 24, 24, 24, 24, 24, 10, 10, 10, 10, 8, 2, 8, 1, 1, 1, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 24, 24, 24, 24, 10, 10, 10, 10, 10, 9, 9] 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]) total number of confs: 84 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187756 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187756/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187756 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 885) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@@H](C)N1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001524187756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524187756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001524187756 none C[C@@H]1CN(c2ccc(C(F)(F)F)cc2)C[C@@H](C)N1C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 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.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: [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, 16, 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, 7, 7, 7, 7, 7, 9, 6, 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 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 9, 12, 26, 26, 12, 21, 26, 26, 26, 26, 26, 12, 12, 12, 12, 7, 2, 7, 1, 1, 1, 10, 10, 10, 10, 10, 12, 12, 12, 12, 12, 26, 26, 26, 26, 12, 12, 12, 12, 12, 10, 10] 39 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]) total number of confs: 162 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187756 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524187756 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187756/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187756/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524187756 Building ZINC001524231208 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524231208' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524231208 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524231208 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524231208/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524231208 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/886 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(Cc2ccc(OC(F)(F)F)cc2)s1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001524231208.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524231208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524231208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524231208 none O=C(Nc1ncc(Cc2ccc(OC(F)(F)F)cc2)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', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', '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, 12, 5, 15, 15, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 2, 8, 8, 8, 8, 8, 31, 31, 31, 31, 8, 8, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524231208 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524231208/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524231208 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 887) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/887 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/887' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(Cc2ccc(OC(F)(F)F)cc2)s1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001524231208.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524231208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524231208/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524231208 none O=C(Nc1ncc(Cc2ccc(OC(F)(F)F)cc2)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', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', '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, 12, 5, 15, 15, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 2, 8, 8, 8, 8, 8, 31, 31, 31, 31, 8, 8, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524231208 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524231208 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524231208/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524231208/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524231208 Building ZINC001524231208 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524231208' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524231208 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524231208 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524231208/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524231208 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 886) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ncc(Cc2ccc(OC(F)(F)F)cc2)s1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001524231208.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524231208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524231208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524231208 none O=C(Nc1ncc(Cc2ccc(OC(F)(F)F)cc2)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', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', '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, 12, 5, 15, 15, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 2, 8, 8, 8, 8, 8, 31, 31, 31, 31, 8, 8, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524231208 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524231208/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524231208 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 887) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ncc(Cc2ccc(OC(F)(F)F)cc2)s1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001524231208.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524231208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524231208/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524231208 none O=C(Nc1ncc(Cc2ccc(OC(F)(F)F)cc2)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', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', '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, 12, 5, 15, 15, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 2, 8, 8, 8, 8, 8, 31, 31, 31, 31, 8, 8, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524231208 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524231208 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524231208/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524231208/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524231208 Building ZINC001524249853 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524249853' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524249853 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524249853 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524249853/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524249853 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/888 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(c2ccc(Br)cc2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC001524249853.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524249853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524249853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524249853 none CC1(c2ccc(Br)cc2)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', 'Br', '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.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, 17, 1, 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: [19, 19, 19, 26, 26, 26, 26, 26, 26, 19, 19, 7, 1, 8, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 19, 19, 19, 19, 19, 26, 26, 26, 26, 19, 19, 19, 19, 6, 10, 10, 10, 10, 10, 10, 10, 10, 19, 19, 19, 19] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 82 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524249853 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524249853/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524249853 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 889) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/889 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/889' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(c2ccc(Br)cc2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC001524249853.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524249853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524249853/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524249853 none CC1(c2ccc(Br)cc2)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', 'Br', '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.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, 17, 1, 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: [18, 18, 18, 24, 24, 24, 24, 24, 24, 18, 18, 8, 1, 7, 1, 1, 1, 6, 6, 12, 12, 6, 12, 12, 12, 18, 18, 18, 18, 18, 24, 24, 24, 24, 18, 18, 18, 18, 6, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 18] 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: 91 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524249853 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524249853 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524249853/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524249853/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524249853 Building ZINC001524249853 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524249853' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524249853 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524249853 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524249853/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524249853 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 888) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC1(c2ccc(Br)cc2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC001524249853.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524249853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524249853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524249853 none CC1(c2ccc(Br)cc2)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', 'Br', '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.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, 17, 1, 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: [19, 19, 19, 26, 26, 26, 26, 26, 26, 19, 19, 7, 1, 8, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 19, 19, 19, 19, 19, 26, 26, 26, 26, 19, 19, 19, 19, 6, 10, 10, 10, 10, 10, 10, 10, 10, 19, 19, 19, 19] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 82 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524249853 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524249853/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524249853 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 889) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CC1(c2ccc(Br)cc2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC001524249853.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524249853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524249853/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524249853 none CC1(c2ccc(Br)cc2)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', 'Br', '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.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, 17, 1, 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: [18, 18, 18, 24, 24, 24, 24, 24, 24, 18, 18, 8, 1, 7, 1, 1, 1, 6, 6, 12, 12, 6, 12, 12, 12, 18, 18, 18, 18, 18, 24, 24, 24, 24, 18, 18, 18, 18, 6, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 18] 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: 91 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524249853 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524249853 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524249853/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524249853/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524249853 Building ZINC001524282200 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001524282200 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/890 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@]2(C1)CCCN(Cc1ccccc1)C2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524282200.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524282200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001524282200 none O=C(N1CC[C@]2(C1)CCCN(Cc1ccccc1)C2)[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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 19, 19, 19, 14, 19, 19, 19, 19, 19, 40, 50, 50, 46, 50, 50, 19, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 19, 19, 19, 19, 19, 18, 19, 19, 19, 19, 19, 19, 40, 40, 50, 50, 50, 50, 50, 19, 19, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 891) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/891 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/891' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@]2(C1)CCCN(Cc1ccccc1)C2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524282200.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524282200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001524282200 none O=C(N1CC[C@]2(C1)CCCN(Cc1ccccc1)C2)[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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 19, 19, 19, 14, 19, 19, 19, 19, 19, 40, 50, 50, 46, 50, 50, 19, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 19, 19, 19, 19, 19, 18, 19, 19, 19, 19, 19, 19, 40, 40, 50, 50, 50, 50, 50, 19, 19, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 892) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/892 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/892' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@]2(C1)CCCN(Cc1ccccc1)C2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524282200.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001524282200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001524282200 none O=C(N1CC[C@]2(C1)CCCN(Cc1ccccc1)C2)[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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 19, 19, 19, 16, 19, 19, 19, 19, 19, 41, 50, 50, 46, 50, 50, 19, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 19, 19, 19, 19, 19, 17, 19, 19, 19, 19, 19, 19, 41, 41, 50, 50, 50, 50, 50, 19, 19, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 893) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/893 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/893' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@]2(C1)CCCN(Cc1ccccc1)C2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524282200.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001524282200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001524282200 none O=C(N1CC[C@]2(C1)CCCN(Cc1ccccc1)C2)[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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 19, 19, 19, 16, 19, 19, 19, 19, 19, 41, 50, 50, 46, 50, 50, 19, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 19, 19, 19, 19, 19, 17, 19, 19, 19, 19, 19, 19, 41, 41, 50, 50, 50, 50, 50, 19, 19, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524282200 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 Building ZINC001524282200 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001524282200 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 890) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CC[C@]2(C1)CCCN(Cc1ccccc1)C2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524282200.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524282200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001524282200 none O=C(N1CC[C@]2(C1)CCCN(Cc1ccccc1)C2)[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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 19, 19, 19, 14, 19, 19, 19, 19, 19, 40, 50, 50, 46, 50, 50, 19, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 19, 19, 19, 19, 19, 18, 19, 19, 19, 19, 19, 19, 40, 40, 50, 50, 50, 50, 50, 19, 19, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 891) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CC[C@]2(C1)CCCN(Cc1ccccc1)C2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524282200.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524282200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001524282200 none O=C(N1CC[C@]2(C1)CCCN(Cc1ccccc1)C2)[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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 19, 19, 19, 14, 19, 19, 19, 19, 19, 40, 50, 50, 46, 50, 50, 19, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 19, 19, 19, 19, 19, 18, 19, 19, 19, 19, 19, 19, 40, 40, 50, 50, 50, 50, 50, 19, 19, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 892) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/892: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@]2(C1)CCCN(Cc1ccccc1)C2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524282200.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001524282200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001524282200 none O=C(N1CC[C@]2(C1)CCCN(Cc1ccccc1)C2)[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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 19, 19, 19, 16, 19, 19, 19, 19, 19, 41, 50, 50, 46, 50, 50, 19, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 19, 19, 19, 19, 19, 17, 19, 19, 19, 19, 19, 19, 41, 41, 50, 50, 50, 50, 50, 19, 19, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 893) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/893: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@]2(C1)CCCN(Cc1ccccc1)C2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524282200.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001524282200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001524282200 none O=C(N1CC[C@]2(C1)CCCN(Cc1ccccc1)C2)[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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 19, 19, 19, 16, 19, 19, 19, 19, 19, 41, 50, 50, 46, 50, 50, 19, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 19, 19, 19, 19, 19, 17, 19, 19, 19, 19, 19, 19, 41, 41, 50, 50, 50, 50, 50, 19, 19, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524282200 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 Building ZINC001524282200 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001524282200 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 890) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CC[C@]2(C1)CCCN(Cc1ccccc1)C2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524282200.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524282200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001524282200 none O=C(N1CC[C@]2(C1)CCCN(Cc1ccccc1)C2)[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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 19, 19, 19, 14, 19, 19, 19, 19, 19, 40, 50, 50, 46, 50, 50, 19, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 19, 19, 19, 19, 19, 18, 19, 19, 19, 19, 19, 19, 40, 40, 50, 50, 50, 50, 50, 19, 19, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 891) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CC[C@]2(C1)CCCN(Cc1ccccc1)C2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524282200.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524282200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001524282200 none O=C(N1CC[C@]2(C1)CCCN(Cc1ccccc1)C2)[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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 19, 19, 19, 14, 19, 19, 19, 19, 19, 40, 50, 50, 46, 50, 50, 19, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 19, 19, 19, 19, 19, 18, 19, 19, 19, 19, 19, 19, 40, 40, 50, 50, 50, 50, 50, 19, 19, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 892) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/892: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@]2(C1)CCCN(Cc1ccccc1)C2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524282200.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001524282200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001524282200 none O=C(N1CC[C@]2(C1)CCCN(Cc1ccccc1)C2)[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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 19, 19, 19, 16, 19, 19, 19, 19, 19, 41, 50, 50, 46, 50, 50, 19, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 19, 19, 19, 19, 19, 17, 19, 19, 19, 19, 19, 19, 41, 41, 50, 50, 50, 50, 50, 19, 19, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 893) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/893: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@]2(C1)CCCN(Cc1ccccc1)C2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524282200.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001524282200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001524282200 none O=C(N1CC[C@]2(C1)CCCN(Cc1ccccc1)C2)[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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 19, 19, 19, 16, 19, 19, 19, 19, 19, 41, 50, 50, 46, 50, 50, 19, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 19, 19, 19, 19, 19, 17, 19, 19, 19, 19, 19, 19, 41, 41, 50, 50, 50, 50, 50, 19, 19, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524282200 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 Building ZINC001524282200 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001524282200 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 890) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CC[C@]2(C1)CCCN(Cc1ccccc1)C2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524282200.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524282200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001524282200 none O=C(N1CC[C@]2(C1)CCCN(Cc1ccccc1)C2)[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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 19, 19, 19, 14, 19, 19, 19, 19, 19, 40, 50, 50, 46, 50, 50, 19, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 19, 19, 19, 19, 19, 18, 19, 19, 19, 19, 19, 19, 40, 40, 50, 50, 50, 50, 50, 19, 19, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 891) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CC[C@]2(C1)CCCN(Cc1ccccc1)C2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524282200.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524282200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001524282200 none O=C(N1CC[C@]2(C1)CCCN(Cc1ccccc1)C2)[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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 19, 19, 19, 14, 19, 19, 19, 19, 19, 40, 50, 50, 46, 50, 50, 19, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 19, 19, 19, 19, 19, 18, 19, 19, 19, 19, 19, 19, 40, 40, 50, 50, 50, 50, 50, 19, 19, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 892) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/892: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@]2(C1)CCCN(Cc1ccccc1)C2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524282200.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001524282200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001524282200 none O=C(N1CC[C@]2(C1)CCCN(Cc1ccccc1)C2)[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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 19, 19, 19, 16, 19, 19, 19, 19, 19, 41, 50, 50, 46, 50, 50, 19, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 19, 19, 19, 19, 19, 17, 19, 19, 19, 19, 19, 19, 41, 41, 50, 50, 50, 50, 50, 19, 19, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 893) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/893: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@]2(C1)CCCN(Cc1ccccc1)C2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524282200.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001524282200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001524282200 none O=C(N1CC[C@]2(C1)CCCN(Cc1ccccc1)C2)[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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 4, 19, 19, 19, 16, 19, 19, 19, 19, 19, 41, 50, 50, 46, 50, 50, 19, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 19, 19, 19, 19, 19, 17, 19, 19, 19, 19, 19, 19, 41, 41, 50, 50, 50, 50, 50, 19, 19, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524282200 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282200 Building ZINC001524282201 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001524282201 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/894 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@]2(C1)CCCN(Cc1ccccc1)C2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524282201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524282201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001524282201 none O=C(N1CC[C@@]2(C1)CCCN(Cc1ccccc1)C2)[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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 43, 50, 50, 43, 50, 50, 23, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 43, 43, 50, 50, 43, 50, 50, 23, 23, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 895) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/895 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/895' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@]2(C1)CCCN(Cc1ccccc1)C2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524282201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524282201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001524282201 none O=C(N1CC[C@@]2(C1)CCCN(Cc1ccccc1)C2)[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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 43, 50, 50, 43, 50, 50, 23, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 43, 43, 50, 50, 43, 50, 50, 23, 23, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 896) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/896 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/896' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@]2(C1)CCCN(Cc1ccccc1)C2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524282201.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001524282201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001524282201 none O=C(N1CC[C@@]2(C1)CCCN(Cc1ccccc1)C2)[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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 21, 21, 21, 20, 21, 21, 21, 21, 21, 39, 50, 50, 39, 50, 50, 21, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 39, 39, 50, 50, 39, 50, 50, 21, 21, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 897) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/897 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/897' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@]2(C1)CCCN(Cc1ccccc1)C2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524282201.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001524282201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001524282201 none O=C(N1CC[C@@]2(C1)CCCN(Cc1ccccc1)C2)[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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 21, 21, 21, 20, 21, 21, 21, 21, 21, 39, 50, 50, 39, 50, 50, 21, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 39, 39, 50, 50, 39, 50, 50, 21, 21, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524282201 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 Building ZINC001524282201 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001524282201 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 894) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CC[C@@]2(C1)CCCN(Cc1ccccc1)C2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524282201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524282201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001524282201 none O=C(N1CC[C@@]2(C1)CCCN(Cc1ccccc1)C2)[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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 43, 50, 50, 43, 50, 50, 23, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 43, 43, 50, 50, 43, 50, 50, 23, 23, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 895) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CC[C@@]2(C1)CCCN(Cc1ccccc1)C2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524282201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524282201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001524282201 none O=C(N1CC[C@@]2(C1)CCCN(Cc1ccccc1)C2)[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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 43, 50, 50, 43, 50, 50, 23, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 43, 43, 50, 50, 43, 50, 50, 23, 23, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 896) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/896: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@]2(C1)CCCN(Cc1ccccc1)C2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524282201.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001524282201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001524282201 none O=C(N1CC[C@@]2(C1)CCCN(Cc1ccccc1)C2)[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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 21, 21, 21, 20, 21, 21, 21, 21, 21, 39, 50, 50, 39, 50, 50, 21, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 39, 39, 50, 50, 39, 50, 50, 21, 21, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 897) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/897: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@]2(C1)CCCN(Cc1ccccc1)C2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524282201.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001524282201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001524282201 none O=C(N1CC[C@@]2(C1)CCCN(Cc1ccccc1)C2)[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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 21, 21, 21, 20, 21, 21, 21, 21, 21, 39, 50, 50, 39, 50, 50, 21, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 39, 39, 50, 50, 39, 50, 50, 21, 21, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524282201 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 Building ZINC001524282201 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001524282201 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 894) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CC[C@@]2(C1)CCCN(Cc1ccccc1)C2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524282201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524282201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001524282201 none O=C(N1CC[C@@]2(C1)CCCN(Cc1ccccc1)C2)[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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 43, 50, 50, 43, 50, 50, 23, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 43, 43, 50, 50, 43, 50, 50, 23, 23, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 895) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CC[C@@]2(C1)CCCN(Cc1ccccc1)C2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524282201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524282201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001524282201 none O=C(N1CC[C@@]2(C1)CCCN(Cc1ccccc1)C2)[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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 43, 50, 50, 43, 50, 50, 23, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 43, 43, 50, 50, 43, 50, 50, 23, 23, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 896) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/896: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@]2(C1)CCCN(Cc1ccccc1)C2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524282201.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001524282201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001524282201 none O=C(N1CC[C@@]2(C1)CCCN(Cc1ccccc1)C2)[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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 21, 21, 21, 20, 21, 21, 21, 21, 21, 39, 50, 50, 39, 50, 50, 21, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 39, 39, 50, 50, 39, 50, 50, 21, 21, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 897) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/897: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@]2(C1)CCCN(Cc1ccccc1)C2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524282201.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001524282201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001524282201 none O=C(N1CC[C@@]2(C1)CCCN(Cc1ccccc1)C2)[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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 21, 21, 21, 20, 21, 21, 21, 21, 21, 39, 50, 50, 39, 50, 50, 21, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 39, 39, 50, 50, 39, 50, 50, 21, 21, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524282201 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 Building ZINC001524282201 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001524282201 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 894) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CC[C@@]2(C1)CCCN(Cc1ccccc1)C2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524282201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524282201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001524282201 none O=C(N1CC[C@@]2(C1)CCCN(Cc1ccccc1)C2)[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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 43, 50, 50, 43, 50, 50, 23, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 43, 43, 50, 50, 43, 50, 50, 23, 23, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 895) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CC[C@@]2(C1)CCCN(Cc1ccccc1)C2)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524282201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524282201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001524282201 none O=C(N1CC[C@@]2(C1)CCCN(Cc1ccccc1)C2)[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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 43, 50, 50, 43, 50, 50, 23, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 43, 43, 50, 50, 43, 50, 50, 23, 23, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 896) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/896: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@]2(C1)CCCN(Cc1ccccc1)C2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524282201.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001524282201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001524282201 none O=C(N1CC[C@@]2(C1)CCCN(Cc1ccccc1)C2)[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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 21, 21, 21, 20, 21, 21, 21, 21, 21, 39, 50, 50, 39, 50, 50, 21, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 39, 39, 50, 50, 39, 50, 50, 21, 21, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 897) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/897: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@]2(C1)CCCN(Cc1ccccc1)C2)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524282201.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001524282201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001524282201 none O=C(N1CC[C@@]2(C1)CCCN(Cc1ccccc1)C2)[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', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 3, 21, 21, 21, 20, 21, 21, 21, 21, 21, 39, 50, 50, 39, 50, 50, 21, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 39, 39, 50, 50, 39, 50, 50, 21, 21, 2, 1, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524282201 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282201 Building ZINC001524282624 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282624' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282624 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524282624 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282624/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282624 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/898 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncc(N(Cc2ccccc2Br)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC001524282624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524282624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001524282624 none Cc1cncc(N(Cc2ccccc2Br)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 17, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 6, 4, 6, 15, 22, 22, 17, 22, 22, 22, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 26, 26, 26, 26, 26, 26, 15, 15, 22, 22, 18, 22, 2, 2, 2, 2, 26] 50 rigid atoms, others: [15, 17, 18, 19] 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: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282624 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282624/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282624 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 899) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/899 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/899' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncc(N(Cc2ccccc2Br)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC001524282624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524282624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001524282624 none Cc1cncc(N(Cc2ccccc2Br)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 17, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 6, 4, 6, 15, 22, 22, 15, 22, 22, 22, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 26, 26, 26, 26, 26, 26, 15, 15, 22, 22, 18, 22, 2, 2, 2, 2, 26] 50 rigid atoms, others: [15, 17, 18, 19] 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: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282624 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524282624 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282624/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282624/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282624 Building ZINC001524282624 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282624' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282624 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524282624 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282624/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282624 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 898) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1cncc(N(Cc2ccccc2Br)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC001524282624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524282624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001524282624 none Cc1cncc(N(Cc2ccccc2Br)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 17, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 6, 4, 6, 15, 22, 22, 17, 22, 22, 22, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 26, 26, 26, 26, 26, 26, 15, 15, 22, 22, 18, 22, 2, 2, 2, 2, 26] 50 rigid atoms, others: [15, 17, 18, 19] 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: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282624 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282624/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282624 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 899) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1cncc(N(Cc2ccccc2Br)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC001524282624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524282624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001524282624 none Cc1cncc(N(Cc2ccccc2Br)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 17, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 6, 4, 6, 15, 22, 22, 15, 22, 22, 22, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 26, 26, 26, 26, 26, 26, 15, 15, 22, 22, 18, 22, 2, 2, 2, 2, 26] 50 rigid atoms, others: [15, 17, 18, 19] 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: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282624 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524282624 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282624/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282624/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524282624 Building ZINC001524283659 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283659' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283659 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524283659 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283659/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283659 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/900 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(F)(c2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524283659.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524283659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001524283659 none O=C(N1CCC(F)(c2ccc(Cl)cc2)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 15, 1, 1, 1, 1, 16, 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] 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, 7, 7] 0 hydrogens 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, 1, 14, 22, 22, 22, 22, 22, 31, 31, 22, 24, 31, 31, 22, 22, 1, 1, 1, 9, 9, 9, 9, 9, 22, 22, 22, 22, 31, 31, 31, 31, 22, 22, 22, 22, 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]) total number of confs: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283659 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283659/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283659 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 901) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/901 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/901' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(F)(c2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524283659.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524283659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001524283659 none O=C(N1CCC(F)(c2ccc(Cl)cc2)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 15, 1, 1, 1, 1, 16, 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] 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, 7, 7] 0 hydrogens 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, 1, 15, 22, 22, 22, 22, 22, 30, 30, 22, 22, 30, 30, 22, 22, 1, 1, 1, 7, 7, 7, 7, 7, 22, 22, 22, 22, 30, 30, 30, 30, 22, 22, 22, 22, 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]) total number of confs: 81 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283659 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524283659 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283659/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283659/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283659 Building ZINC001524283659 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283659' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283659 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524283659 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283659/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283659 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 900) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CCC(F)(c2ccc(Cl)cc2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524283659.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524283659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001524283659 none O=C(N1CCC(F)(c2ccc(Cl)cc2)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 15, 1, 1, 1, 1, 16, 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] 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, 7, 7] 0 hydrogens 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, 1, 14, 22, 22, 22, 22, 22, 31, 31, 22, 24, 31, 31, 22, 22, 1, 1, 1, 9, 9, 9, 9, 9, 22, 22, 22, 22, 31, 31, 31, 31, 22, 22, 22, 22, 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]) total number of confs: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283659 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283659/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283659 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 901) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CCC(F)(c2ccc(Cl)cc2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524283659.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524283659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001524283659 none O=C(N1CCC(F)(c2ccc(Cl)cc2)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 15, 1, 1, 1, 1, 16, 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] 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, 7, 7] 0 hydrogens 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, 1, 15, 22, 22, 22, 22, 22, 30, 30, 22, 22, 30, 30, 22, 22, 1, 1, 1, 7, 7, 7, 7, 7, 22, 22, 22, 22, 30, 30, 30, 30, 22, 22, 22, 22, 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]) total number of confs: 81 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283659 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524283659 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283659/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283659/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283659 Building ZINC001524283904 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283904' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283904 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524283904 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283904/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283904 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/902 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(F)(c2ccc(Cl)cc2)CC1) `ZINC001524283904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524283904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001524283904 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(F)(c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', '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'] 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, 15, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 11, 11, 5, 11, 11, 4, 4, 1, 1, 1, 1, 8, 12, 18, 18, 18, 18, 18, 22, 22, 18, 19, 22, 22, 18, 18, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 4, 18, 18, 18, 18, 22, 22, 22, 22, 18, 18, 18, 18] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283904 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283904/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283904 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 903) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/903 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/903' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(F)(c2ccc(Cl)cc2)CC1) `ZINC001524283904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524283904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001524283904 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(F)(c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', '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'] 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, 15, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 5, 10, 10, 3, 3, 1, 1, 1, 1, 8, 13, 19, 19, 19, 19, 19, 25, 25, 19, 21, 25, 25, 19, 19, 3, 3, 3, 10, 10, 6, 10, 10, 3, 3, 3, 19, 19, 19, 19, 25, 25, 25, 25, 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]) total number of confs: 87 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283904 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524283904 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283904/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283904/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283904 Building ZINC001524283904 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283904' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283904 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524283904 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283904/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283904 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 902) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(F)(c2ccc(Cl)cc2)CC1) `ZINC001524283904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524283904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001524283904 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(F)(c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', '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'] 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, 15, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 11, 11, 5, 11, 11, 4, 4, 1, 1, 1, 1, 8, 12, 18, 18, 18, 18, 18, 22, 22, 18, 19, 22, 22, 18, 18, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 4, 18, 18, 18, 18, 22, 22, 22, 22, 18, 18, 18, 18] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283904 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283904/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283904 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 903) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(F)(c2ccc(Cl)cc2)CC1) `ZINC001524283904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524283904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001524283904 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(F)(c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', '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'] 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, 15, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 5, 10, 10, 3, 3, 1, 1, 1, 1, 8, 13, 19, 19, 19, 19, 19, 25, 25, 19, 21, 25, 25, 19, 19, 3, 3, 3, 10, 10, 6, 10, 10, 3, 3, 3, 19, 19, 19, 19, 25, 25, 25, 25, 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]) total number of confs: 87 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283904 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524283904 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283904/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283904/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524283904 Building ZINC001524356396 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524356396' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524356396 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524356396 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524356396/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524356396 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/904 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc2c(cc1Br)CCC2)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524356396.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524356396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524356396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001524356396 none O=C(Nc1cc2c(cc1Br)CCC2)[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', 'Br', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 17, 5, 5, 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, 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: [7, 1, 7, 7, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 12, 12, 12, 12, 12, 7, 31, 31, 31, 31, 31, 31, 31, 31, 12, 12] 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524356396 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524356396/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524356396 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 905) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/905 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/905' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc2c(cc1Br)CCC2)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524356396.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524356396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524356396/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001524356396 none O=C(Nc1cc2c(cc1Br)CCC2)[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', 'Br', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 17, 5, 5, 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, 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: [8, 1, 8, 8, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 12, 12, 12, 12, 12, 8, 31, 31, 31, 31, 31, 31, 31, 31, 12, 12] 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524356396 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524356396 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524356396/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524356396/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524356396 Building ZINC001524356396 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524356396' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524356396 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524356396 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524356396/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524356396 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 904) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1cc2c(cc1Br)CCC2)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524356396.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524356396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524356396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001524356396 none O=C(Nc1cc2c(cc1Br)CCC2)[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', 'Br', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 17, 5, 5, 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, 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: [7, 1, 7, 7, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 12, 12, 12, 12, 12, 7, 31, 31, 31, 31, 31, 31, 31, 31, 12, 12] 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524356396 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524356396/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524356396 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 905) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1cc2c(cc1Br)CCC2)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524356396.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524356396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524356396/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001524356396 none O=C(Nc1cc2c(cc1Br)CCC2)[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', 'Br', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 17, 5, 5, 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, 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: [8, 1, 8, 8, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 12, 12, 12, 12, 12, 8, 31, 31, 31, 31, 31, 31, 31, 31, 12, 12] 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524356396 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524356396 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524356396/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524356396/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524356396 Building ZINC001524378530 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524378530' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524378530 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524378530 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524378530/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524378530 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/906 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(Br)cc2sc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)nc21) `ZINC001524378530.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524378530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524378530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001524378530 none CCc1cc(Br)cc2sc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)nc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', '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', 'N.2', '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, 1, 1, 1, 17, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 10, 10, 6, 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524378530 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524378530/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524378530 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 907) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/907 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/907' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(Br)cc2sc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)nc21) `ZINC001524378530.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524378530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524378530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001524378530 none CCc1cc(Br)cc2sc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)nc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', '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', 'N.2', '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, 1, 1, 1, 17, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 9, 6, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 9, 9, 19, 19, 19, 19, 19, 9, 9, 6, 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524378530 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524378530 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524378530/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524378530/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524378530 Building ZINC001524378530 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524378530' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524378530 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524378530 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524378530/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524378530 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 906) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCc1cc(Br)cc2sc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)nc21) `ZINC001524378530.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524378530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524378530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001524378530 none CCc1cc(Br)cc2sc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)nc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', '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', 'N.2', '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, 1, 1, 1, 17, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 10, 10, 6, 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524378530 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524378530/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524378530 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 907) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCc1cc(Br)cc2sc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)nc21) `ZINC001524378530.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524378530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524378530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001524378530 none CCc1cc(Br)cc2sc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)nc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', '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', 'N.2', '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, 1, 1, 1, 17, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 9, 6, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 9, 9, 19, 19, 19, 19, 19, 9, 9, 6, 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524378530 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524378530 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524378530/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524378530/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524378530 Building ZINC001524427753 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524427753' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524427753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524427753 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524427753/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524427753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/908 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(n2ccc(C(F)(F)F)n2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524427753.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524427753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524427753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524427753 none O=C(Nc1ccc(n2ccc(C(F)(F)F)n2)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', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 1, 1, 5, 15, 15, 15, 8, 1, 1, 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: [5, 1, 5, 5, 15, 15, 5, 8, 31, 31, 31, 34, 34, 34, 34, 31, 15, 15, 1, 1, 1, 12, 12, 12, 12, 12, 5, 15, 15, 31, 34, 15, 15, 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: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524427753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524427753/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524427753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 909) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/909 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/909' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(n2ccc(C(F)(F)F)n2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524427753.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524427753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524427753/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524427753 none O=C(Nc1ccc(n2ccc(C(F)(F)F)n2)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', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 1, 1, 5, 15, 15, 15, 8, 1, 1, 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: [6, 1, 6, 6, 16, 16, 8, 10, 31, 34, 34, 34, 34, 34, 34, 31, 16, 16, 1, 1, 1, 12, 12, 12, 12, 12, 6, 16, 16, 31, 34, 16, 16, 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: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524427753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524427753 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524427753/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524427753/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524427753 Building ZINC001524427753 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524427753' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524427753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524427753 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524427753/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524427753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 908) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ccc(n2ccc(C(F)(F)F)n2)cc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524427753.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524427753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524427753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524427753 none O=C(Nc1ccc(n2ccc(C(F)(F)F)n2)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', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 1, 1, 5, 15, 15, 15, 8, 1, 1, 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: [5, 1, 5, 5, 15, 15, 5, 8, 31, 31, 31, 34, 34, 34, 34, 31, 15, 15, 1, 1, 1, 12, 12, 12, 12, 12, 5, 15, 15, 31, 34, 15, 15, 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: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524427753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524427753/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524427753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 909) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ccc(n2ccc(C(F)(F)F)n2)cc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524427753.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524427753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524427753/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524427753 none O=C(Nc1ccc(n2ccc(C(F)(F)F)n2)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', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 1, 1, 5, 15, 15, 15, 8, 1, 1, 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: [6, 1, 6, 6, 16, 16, 8, 10, 31, 34, 34, 34, 34, 34, 34, 31, 16, 16, 1, 1, 1, 12, 12, 12, 12, 12, 6, 16, 16, 31, 34, 16, 16, 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: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524427753 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524427753 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524427753/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524427753/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524427753 Building ZINC001524432634 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524432634' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524432634 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524432634 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524432634/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524432634 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/910 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OCC(F)(F)F)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524432634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524432634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524432634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524432634 none O=C(Nc1ccc(OCC(F)(F)F)c(Cl)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', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 16, 1, 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, 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: [2, 1, 2, 2, 8, 8, 8, 8, 31, 50, 50, 50, 50, 8, 8, 8, 1, 1, 1, 3, 3, 3, 3, 3, 2, 8, 8, 50, 50, 8, 3, 3] 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: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524432634 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524432634/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524432634 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 911) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/911 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/911' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(OCC(F)(F)F)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524432634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524432634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524432634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524432634 none O=C(Nc1ccc(OCC(F)(F)F)c(Cl)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', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 16, 1, 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, 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: [2, 1, 2, 2, 8, 8, 8, 8, 31, 50, 50, 50, 50, 8, 8, 8, 1, 1, 1, 3, 3, 3, 3, 3, 2, 8, 8, 50, 50, 8, 3, 3] 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: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524432634 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524432634 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524432634/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524432634/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524432634 Building ZINC001524432634 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524432634' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524432634 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524432634 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524432634/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524432634 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 910) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(Nc1ccc(OCC(F)(F)F)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524432634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524432634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524432634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524432634 none O=C(Nc1ccc(OCC(F)(F)F)c(Cl)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', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 16, 1, 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, 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: [2, 1, 2, 2, 8, 8, 8, 8, 31, 50, 50, 50, 50, 8, 8, 8, 1, 1, 1, 3, 3, 3, 3, 3, 2, 8, 8, 50, 50, 8, 3, 3] 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: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524432634 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524432634/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524432634 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 911) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(Nc1ccc(OCC(F)(F)F)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524432634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524432634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524432634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524432634 none O=C(Nc1ccc(OCC(F)(F)F)c(Cl)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', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 16, 1, 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, 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: [2, 1, 2, 2, 8, 8, 8, 8, 31, 50, 50, 50, 50, 8, 8, 8, 1, 1, 1, 3, 3, 3, 3, 3, 2, 8, 8, 50, 50, 8, 3, 3] 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: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524432634 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524432634 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524432634/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524432634/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524432634 Building ZINC001524474482 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474482' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474482 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524474482 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474482/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474482 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/912 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc([C@H]2CN(C(=O)OC(C)(C)C)CCN2C(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)cc1) `ZINC001524474482.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524474482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC001524474482 none CCc1ccc([C@H]2CN(C(=O)OC(C)(C)C)CCN2C(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', '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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 25, 25, 8, 8, 8, 8, 8, 8, 22, 22, 35, 39, 39, 39, 8, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 39, 39, 39, 39, 39, 39, 39, 39, 39, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 25, 25] 50 rigid atoms, others: [59, 60, 55, 61, 56, 58, 20, 57, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 62, 63]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474482 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474482/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474482 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 913) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/913 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/913' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc([C@H]2CN(C(=O)OC(C)(C)C)CCN2C(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)cc1) `ZINC001524474482.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524474482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC001524474482 none CCc1ccc([C@H]2CN(C(=O)OC(C)(C)C)CCN2C(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', '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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 19, 19, 7, 7, 7, 7, 7, 7, 17, 17, 32, 37, 37, 37, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 7, 37, 37, 37, 37, 37, 37, 37, 37, 37, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 19, 19] 50 rigid atoms, others: [59, 60, 55, 61, 56, 58, 57, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 62, 63]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474482 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524474482 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474482/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474482/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474482 Building ZINC001524474482 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474482' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474482 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524474482 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474482/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474482 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 912) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCc1ccc([C@H]2CN(C(=O)OC(C)(C)C)CCN2C(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)cc1) `ZINC001524474482.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524474482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC001524474482 none CCc1ccc([C@H]2CN(C(=O)OC(C)(C)C)CCN2C(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', '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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 25, 25, 8, 8, 8, 8, 8, 8, 22, 22, 35, 39, 39, 39, 8, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 39, 39, 39, 39, 39, 39, 39, 39, 39, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 25, 25] 50 rigid atoms, others: [59, 60, 55, 61, 56, 58, 20, 57, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 62, 63]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474482 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474482/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474482 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 913) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCc1ccc([C@H]2CN(C(=O)OC(C)(C)C)CCN2C(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)cc1) `ZINC001524474482.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524474482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC001524474482 none CCc1ccc([C@H]2CN(C(=O)OC(C)(C)C)CCN2C(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', '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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 19, 19, 7, 7, 7, 7, 7, 7, 17, 17, 32, 37, 37, 37, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 7, 37, 37, 37, 37, 37, 37, 37, 37, 37, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 19, 19] 50 rigid atoms, others: [59, 60, 55, 61, 56, 58, 57, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 62, 63]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474482 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524474482 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474482/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474482/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474482 Building ZINC001524474484 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474484' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474484 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524474484 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474484/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474484 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/914 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc([C@@H]2CN(C(=O)OC(C)(C)C)CCN2C(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)cc1) `ZINC001524474484.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524474484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC001524474484 none CCc1ccc([C@@H]2CN(C(=O)OC(C)(C)C)CCN2C(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', '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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 19, 19, 36, 39, 39, 39, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 7, 39, 39, 39, 39, 39, 39, 39, 39, 39, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 19, 19] 50 rigid atoms, others: [59, 60, 55, 61, 56, 58, 57, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 62, 63]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474484 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474484/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474484 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 915) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/915 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/915' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc([C@@H]2CN(C(=O)OC(C)(C)C)CCN2C(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)cc1) `ZINC001524474484.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524474484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC001524474484 none CCc1ccc([C@@H]2CN(C(=O)OC(C)(C)C)CCN2C(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', '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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 13, 24, 24, 9, 9, 9, 9, 9, 9, 18, 18, 34, 37, 37, 37, 9, 9, 8, 2, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 37, 37, 37, 37, 37, 37, 37, 37, 37, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 24, 24] 50 rigid atoms, others: [59, 60, 55, 61, 56, 58, 57, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 62, 63]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474484 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524474484 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474484/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474484/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474484 Building ZINC001524474484 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474484' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474484 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524474484 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474484/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474484 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 914) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCc1ccc([C@@H]2CN(C(=O)OC(C)(C)C)CCN2C(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)cc1) `ZINC001524474484.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524474484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC001524474484 none CCc1ccc([C@@H]2CN(C(=O)OC(C)(C)C)CCN2C(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', '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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 19, 19, 36, 39, 39, 39, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 7, 7, 39, 39, 39, 39, 39, 39, 39, 39, 39, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 19, 19] 50 rigid atoms, others: [59, 60, 55, 61, 56, 58, 57, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 62, 63]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474484 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474484/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474484 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 915) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCc1ccc([C@@H]2CN(C(=O)OC(C)(C)C)CCN2C(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)cc1) `ZINC001524474484.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524474484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC001524474484 none CCc1ccc([C@@H]2CN(C(=O)OC(C)(C)C)CCN2C(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', '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', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 13, 24, 24, 9, 9, 9, 9, 9, 9, 18, 18, 34, 37, 37, 37, 9, 9, 8, 2, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 37, 37, 37, 37, 37, 37, 37, 37, 37, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 24, 24] 50 rigid atoms, others: [59, 60, 55, 61, 56, 58, 57, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 62, 63]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474484 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524474484 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474484/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474484/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524474484 Building ZINC001524518427 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524518427' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524518427 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524518427 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524518427/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524518427 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/916 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc2ccccc2c1) `ZINC001524518427.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524518427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524518427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524518427 none COC(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc2ccccc2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 24, 5, 3, 5, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 24, 24, 24, 11, 11, 3, 3, 1, 3, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 113 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524518427 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524518427/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524518427 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 917) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/917 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/917' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc2ccccc2c1) `ZINC001524518427.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524518427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524518427/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524518427 none COC(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc2ccccc2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 25, 6, 4, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 25, 25, 25, 14, 14, 4, 3, 1, 3, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524518427 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524518427 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524518427/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524518427/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524518427 Building ZINC001524518427 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524518427' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524518427 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524518427 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524518427/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524518427 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 916) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COC(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc2ccccc2c1) `ZINC001524518427.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524518427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524518427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524518427 none COC(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc2ccccc2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 24, 5, 3, 5, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 24, 24, 24, 11, 11, 3, 3, 1, 3, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 113 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524518427 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524518427/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524518427 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 917) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COC(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc2ccccc2c1) `ZINC001524518427.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524518427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524518427/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524518427 none COC(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc2ccccc2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 25, 6, 4, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 25, 25, 25, 14, 14, 4, 3, 1, 3, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524518427 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524518427 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524518427/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524518427/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524518427 Building ZINC001524656214 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524656214' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524656214 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524656214 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524656214/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524656214 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/918 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Br)c2cccnc12)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524656214.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524656214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524656214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524656214 none O=C(Nc1ccc(Br)c2cccnc12)[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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 8, 1, 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, 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: [7, 1, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 12, 12, 12, 12, 12, 7, 28, 28, 28, 28, 28, 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: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524656214 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524656214/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524656214 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 919) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/919 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/919' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Br)c2cccnc12)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524656214.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524656214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524656214/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524656214 none O=C(Nc1ccc(Br)c2cccnc12)[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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 8, 1, 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, 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: [7, 1, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 12, 12, 12, 12, 12, 7, 28, 28, 28, 28, 28, 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: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524656214 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524656214 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524656214/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524656214/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524656214 Building ZINC001524656214 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524656214' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524656214 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524656214 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524656214/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524656214 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 918) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ccc(Br)c2cccnc12)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524656214.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524656214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524656214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524656214 none O=C(Nc1ccc(Br)c2cccnc12)[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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 8, 1, 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, 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: [7, 1, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 12, 12, 12, 12, 12, 7, 28, 28, 28, 28, 28, 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: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524656214 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524656214/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524656214 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 919) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ccc(Br)c2cccnc12)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524656214.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524656214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524656214/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524656214 none O=C(Nc1ccc(Br)c2cccnc12)[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', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 8, 1, 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, 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: [7, 1, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 12, 12, 12, 12, 12, 7, 28, 28, 28, 28, 28, 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: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524656214 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524656214 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524656214/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524656214/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524656214 Building ZINC001524692038 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524692038' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524692038 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524692038 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524692038/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524692038 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/920 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccc(C(F)(F)F)cc1)C1CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524692038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524692038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524692038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001524692038 none O=C(N(Cc1ccc(C(F)(F)F)cc1)C1CC1)[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', 'F', 'F', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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] 0 hydrogens 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, 28, 34, 34, 29, 34, 34, 34, 34, 34, 34, 12, 20, 20, 1, 1, 1, 4, 4, 4, 4, 4, 28, 28, 34, 34, 34, 34, 20, 20, 20, 20, 20, 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]) total number of confs: 163 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524692038 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524692038/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524692038 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 921) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/921 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/921' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccc(C(F)(F)F)cc1)C1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524692038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524692038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524692038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001524692038 none O=C(N(Cc1ccc(C(F)(F)F)cc1)C1CC1)[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', 'F', 'F', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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] 0 hydrogens 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, 26, 33, 33, 33, 33, 33, 33, 33, 33, 33, 12, 19, 19, 1, 1, 1, 4, 4, 4, 4, 4, 26, 26, 33, 33, 33, 33, 19, 19, 19, 19, 19, 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]) total number of confs: 148 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524692038 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524692038 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524692038/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524692038/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524692038 Building ZINC001524692038 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524692038' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524692038 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524692038 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524692038/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524692038 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 920) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N(Cc1ccc(C(F)(F)F)cc1)C1CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524692038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524692038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524692038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001524692038 none O=C(N(Cc1ccc(C(F)(F)F)cc1)C1CC1)[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', 'F', 'F', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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] 0 hydrogens 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, 28, 34, 34, 29, 34, 34, 34, 34, 34, 34, 12, 20, 20, 1, 1, 1, 4, 4, 4, 4, 4, 28, 28, 34, 34, 34, 34, 20, 20, 20, 20, 20, 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]) total number of confs: 163 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524692038 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524692038/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524692038 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 921) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N(Cc1ccc(C(F)(F)F)cc1)C1CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524692038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524692038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524692038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001524692038 none O=C(N(Cc1ccc(C(F)(F)F)cc1)C1CC1)[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', 'F', 'F', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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] 0 hydrogens 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, 26, 33, 33, 33, 33, 33, 33, 33, 33, 33, 12, 19, 19, 1, 1, 1, 4, 4, 4, 4, 4, 26, 26, 33, 33, 33, 33, 19, 19, 19, 19, 19, 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]) total number of confs: 148 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524692038 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524692038 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524692038/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524692038/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524692038 Building ZINC001524709374 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524709374' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524709374 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524709374 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524709374/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524709374 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/922 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(F)(c2ccccc2OC(F)(F)F)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001524709374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524709374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524709374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524709374 none O=C(N1CCC(F)(c2ccccc2OC(F)(F)F)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 15, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 1, 1, 16, 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, 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, 6, 9, 9, 9, 9, 9, 22, 22, 11, 22, 22, 22, 35, 35, 35, 35, 9, 9, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 9, 9, 22, 22, 22, 22, 9, 9, 9, 9, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524709374 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524709374/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524709374 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 923) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/923 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/923' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(F)(c2ccccc2OC(F)(F)F)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001524709374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524709374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524709374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524709374 none O=C(N1CCC(F)(c2ccccc2OC(F)(F)F)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 15, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 1, 1, 16, 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, 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: [3, 1, 4, 5, 5, 5, 5, 5, 16, 16, 7, 16, 16, 16, 29, 29, 29, 29, 5, 5, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 5, 5, 16, 16, 16, 16, 5, 5, 5, 5, 3, 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: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524709374 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524709374 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524709374/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524709374/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524709374 Building ZINC001524709374 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524709374' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524709374 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524709374 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524709374/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524709374 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 922) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CCC(F)(c2ccccc2OC(F)(F)F)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001524709374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524709374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524709374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524709374 none O=C(N1CCC(F)(c2ccccc2OC(F)(F)F)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 15, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 1, 1, 16, 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, 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, 6, 9, 9, 9, 9, 9, 22, 22, 11, 22, 22, 22, 35, 35, 35, 35, 9, 9, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 9, 9, 22, 22, 22, 22, 9, 9, 9, 9, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524709374 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524709374/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524709374 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 923) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(N1CCC(F)(c2ccccc2OC(F)(F)F)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001524709374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524709374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524709374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524709374 none O=C(N1CCC(F)(c2ccccc2OC(F)(F)F)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 15, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 5, 5, 5, 12, 1, 1, 1, 1, 16, 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, 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: [3, 1, 4, 5, 5, 5, 5, 5, 16, 16, 7, 16, 16, 16, 29, 29, 29, 29, 5, 5, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 5, 5, 16, 16, 16, 16, 5, 5, 5, 5, 3, 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: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524709374 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524709374 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524709374/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524709374/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524709374 Building ZINC001524736425 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524736425' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524736425 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524736425 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524736425/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524736425 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/924 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/924' -> `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)NCCCc1ccc(Cl)cc1Cl) `ZINC001524736425.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524736425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524736425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001524736425 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCc1ccc(Cl)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.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'] 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, 16, 1, 1, 16, 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] 0 hydrogens need rotated 50 conformations in 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, 17, 24, 34, 44, 44, 34, 44, 44, 44, 44, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 17, 17, 34, 34, 34, 34, 44, 44, 44] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 278 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524736425 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524736425/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524736425 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 925) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/925 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/925' -> `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)NCCCc1ccc(Cl)cc1Cl) `ZINC001524736425.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524736425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524736425/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001524736425 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCc1ccc(Cl)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.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'] 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, 16, 1, 1, 16, 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] 0 hydrogens need rotated 50 conformations in 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, 4, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 17, 24, 34, 44, 44, 44, 44, 44, 44, 44, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 3, 17, 17, 34, 34, 34, 34, 44, 44, 44] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 227 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524736425 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524736425 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524736425/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524736425/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524736425 Building ZINC001524736425 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524736425' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524736425 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524736425 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524736425/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524736425 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 924) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCc1ccc(Cl)cc1Cl) `ZINC001524736425.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524736425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524736425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001524736425 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCc1ccc(Cl)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.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'] 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, 16, 1, 1, 16, 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] 0 hydrogens need rotated 50 conformations in 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, 17, 24, 34, 44, 44, 34, 44, 44, 44, 44, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 17, 17, 34, 34, 34, 34, 44, 44, 44] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 278 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524736425 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524736425/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524736425 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 925) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCc1ccc(Cl)cc1Cl) `ZINC001524736425.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524736425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524736425/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001524736425 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCc1ccc(Cl)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.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'] 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, 16, 1, 1, 16, 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] 0 hydrogens need rotated 50 conformations in 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, 4, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 17, 24, 34, 44, 44, 44, 44, 44, 44, 44, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 3, 17, 17, 34, 34, 34, 34, 44, 44, 44] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 227 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524736425 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524736425 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524736425/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524736425/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524736425 Building ZINC001524781209 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524781209' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524781209 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524781209 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524781209/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524781209 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/926 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(Br)ccc2c1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)CCC2) `ZINC001524781209.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524781209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524781209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001524781209 none Cc1c(Br)ccc2c1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Br', '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.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 7, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 15 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]) total number of confs: 23 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524781209 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524781209/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524781209 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 927) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/927 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/927' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(Br)ccc2c1N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)CCC2) `ZINC001524781209.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524781209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524781209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001524781209 none Cc1c(Br)ccc2c1N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Br', '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.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 7, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 15 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]) total number of confs: 23 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524781209 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524781209 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524781209/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524781209/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524781209 Building ZINC001524781209 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524781209' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524781209 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524781209 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524781209/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524781209 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 926) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1c(Br)ccc2c1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)CCC2) `ZINC001524781209.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524781209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524781209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001524781209 none Cc1c(Br)ccc2c1N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Br', '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.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 7, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 15 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]) total number of confs: 23 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524781209 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524781209/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524781209 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 927) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1c(Br)ccc2c1N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)CCC2) `ZINC001524781209.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524781209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524781209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC001524781209 none Cc1c(Br)ccc2c1N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Br', '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.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 7, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 15 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]) total number of confs: 23 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524781209 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524781209 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524781209/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524781209/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524781209 Building ZINC001524783737 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783737' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783737 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524783737 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783737/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783737 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/928 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ccc(Br)c(C)c2)cc1Cl) `ZINC001524783737.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524783737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001524783737 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ccc(Br)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.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 5, 1, 1, 1, 16, 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, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 9, 26, 26, 17, 26, 26, 26, 26, 4, 4, 4, 8, 8, 8, 4, 4, 9, 9, 9, 9, 9, 9, 26, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783737 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783737/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783737 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 929) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/929 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/929' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ccc(Br)c(C)c2)cc1Cl) `ZINC001524783737.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524783737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783737/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001524783737 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ccc(Br)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.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 5, 1, 1, 1, 16, 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, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 26, 26, 10, 26, 26, 26, 26, 4, 4, 4, 9, 9, 9, 4, 4, 5, 5, 5, 5, 5, 5, 26, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783737 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524783737 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783737/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783737/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783737 Building ZINC001524783737 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783737' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783737 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524783737 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783737/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783737 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 928) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ccc(Br)c(C)c2)cc1Cl) `ZINC001524783737.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524783737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001524783737 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ccc(Br)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.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 5, 1, 1, 1, 16, 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, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 9, 26, 26, 17, 26, 26, 26, 26, 4, 4, 4, 8, 8, 8, 4, 4, 9, 9, 9, 9, 9, 9, 26, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783737 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783737/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783737 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 929) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ccc(Br)c(C)c2)cc1Cl) `ZINC001524783737.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524783737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783737/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001524783737 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2c2ccc(Br)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.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 5, 1, 1, 1, 16, 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, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 26, 26, 10, 26, 26, 26, 26, 4, 4, 4, 9, 9, 9, 4, 4, 5, 5, 5, 5, 5, 5, 26, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783737 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524783737 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783737/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783737/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783737 Building ZINC001524783738 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783738' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783738 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524783738 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783738/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783738 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/930 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ccc(Br)c(C)c2)cc1Cl) `ZINC001524783738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524783738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001524783738 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ccc(Br)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.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 5, 1, 1, 1, 16, 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, 4, 3, 4, 4, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 9, 9, 9, 4, 4, 5, 5, 5, 5, 5, 5, 25, 25, 25, 25, 25, 25, 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783738 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783738/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783738 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 931) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/931 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/931' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ccc(Br)c(C)c2)cc1Cl) `ZINC001524783738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524783738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001524783738 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ccc(Br)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.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 5, 1, 1, 1, 16, 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, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 9, 27, 27, 14, 17, 27, 27, 27, 4, 4, 4, 9, 9, 9, 4, 4, 9, 9, 9, 9, 9, 9, 27, 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783738 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524783738 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783738/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783738/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783738 Building ZINC001524783738 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783738' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783738 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524783738 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783738/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783738 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 930) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ccc(Br)c(C)c2)cc1Cl) `ZINC001524783738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524783738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001524783738 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ccc(Br)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.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 5, 1, 1, 1, 16, 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, 4, 3, 4, 4, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 9, 9, 9, 4, 4, 5, 5, 5, 5, 5, 5, 25, 25, 25, 25, 25, 25, 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783738 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783738/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783738 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 931) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ccc(Br)c(C)c2)cc1Cl) `ZINC001524783738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524783738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001524783738 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2c2ccc(Br)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.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 5, 1, 1, 1, 16, 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, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 9, 9, 27, 27, 14, 17, 27, 27, 27, 4, 4, 4, 9, 9, 9, 4, 4, 9, 9, 9, 9, 9, 9, 27, 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783738 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524783738 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783738/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783738/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524783738 Building ZINC001524790581 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001524790581 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/932 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001524790581.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524790581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001524790581 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 9, 11, 11, 11, 11, 11, 11, 11, 16, 26, 26, 26, 26, 26, 41, 50, 50, 45, 50, 50, 26, 26, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 26, 26, 26, 26, 41, 41, 50, 50, 45, 50, 50, 26, 26, 26, 26] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 186 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 933) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/933 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/933' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001524790581.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524790581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001524790581 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 4, 4, 4, 6, 19, 19, 19, 19, 19, 38, 47, 47, 44, 47, 47, 19, 19, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 38, 38, 47, 47, 47, 47, 47, 19, 19, 19, 19] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 187 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 934) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/934 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/934' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001524790581.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001524790581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001524790581 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 9, 9, 11, 11, 11, 11, 11, 11, 11, 15, 25, 25, 25, 25, 25, 40, 50, 50, 40, 50, 50, 25, 25, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 25, 25, 25, 25, 40, 40, 50, 50, 45, 50, 50, 25, 25, 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, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 214 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 935) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/935 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/935' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001524790581.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001524790581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001524790581 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 4, 4, 4, 6, 19, 19, 19, 19, 19, 38, 47, 47, 38, 47, 47, 19, 19, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 38, 38, 47, 47, 38, 47, 47, 19, 19, 19, 19] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 199 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524790581 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 Building ZINC001524790581 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001524790581 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 932) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001524790581.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524790581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001524790581 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 9, 11, 11, 11, 11, 11, 11, 11, 16, 26, 26, 26, 26, 26, 41, 50, 50, 45, 50, 50, 26, 26, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 26, 26, 26, 26, 41, 41, 50, 50, 45, 50, 50, 26, 26, 26, 26] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 186 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 933) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001524790581.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524790581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001524790581 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 4, 4, 4, 6, 19, 19, 19, 19, 19, 38, 47, 47, 44, 47, 47, 19, 19, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 38, 38, 47, 47, 47, 47, 47, 19, 19, 19, 19] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 187 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 934) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/934: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001524790581.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001524790581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001524790581 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 9, 9, 11, 11, 11, 11, 11, 11, 11, 15, 25, 25, 25, 25, 25, 40, 50, 50, 40, 50, 50, 25, 25, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 25, 25, 25, 25, 40, 40, 50, 50, 45, 50, 50, 25, 25, 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, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 214 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 935) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/935: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001524790581.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001524790581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001524790581 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 4, 4, 4, 6, 19, 19, 19, 19, 19, 38, 47, 47, 38, 47, 47, 19, 19, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 38, 38, 47, 47, 38, 47, 47, 19, 19, 19, 19] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 199 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524790581 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 Building ZINC001524790581 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001524790581 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 932) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001524790581.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524790581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001524790581 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 9, 11, 11, 11, 11, 11, 11, 11, 16, 26, 26, 26, 26, 26, 41, 50, 50, 45, 50, 50, 26, 26, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 26, 26, 26, 26, 41, 41, 50, 50, 45, 50, 50, 26, 26, 26, 26] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 186 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 933) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001524790581.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524790581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001524790581 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 4, 4, 4, 6, 19, 19, 19, 19, 19, 38, 47, 47, 44, 47, 47, 19, 19, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 38, 38, 47, 47, 47, 47, 47, 19, 19, 19, 19] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 187 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 934) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/934: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001524790581.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001524790581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001524790581 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 9, 9, 11, 11, 11, 11, 11, 11, 11, 15, 25, 25, 25, 25, 25, 40, 50, 50, 40, 50, 50, 25, 25, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 25, 25, 25, 25, 40, 40, 50, 50, 45, 50, 50, 25, 25, 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, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 214 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 935) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/935: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001524790581.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001524790581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001524790581 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 4, 4, 4, 6, 19, 19, 19, 19, 19, 38, 47, 47, 38, 47, 47, 19, 19, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 38, 38, 47, 47, 38, 47, 47, 19, 19, 19, 19] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 199 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524790581 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 Building ZINC001524790581 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001524790581 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 932) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001524790581.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524790581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001524790581 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 9, 11, 11, 11, 11, 11, 11, 11, 16, 26, 26, 26, 26, 26, 41, 50, 50, 45, 50, 50, 26, 26, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 26, 26, 26, 26, 41, 41, 50, 50, 45, 50, 50, 26, 26, 26, 26] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 186 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 933) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001524790581.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524790581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001524790581 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 4, 4, 4, 6, 19, 19, 19, 19, 19, 38, 47, 47, 44, 47, 47, 19, 19, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 38, 38, 47, 47, 47, 47, 47, 19, 19, 19, 19] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 187 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 934) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/934: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001524790581.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001524790581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001524790581 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 9, 9, 11, 11, 11, 11, 11, 11, 11, 15, 25, 25, 25, 25, 25, 40, 50, 50, 40, 50, 50, 25, 25, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 25, 25, 25, 25, 40, 40, 50, 50, 45, 50, 50, 25, 25, 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, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 214 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 935) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/935: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001524790581.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001524790581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001524790581 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 4, 4, 4, 4, 4, 6, 19, 19, 19, 19, 19, 38, 47, 47, 38, 47, 47, 19, 19, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 38, 38, 47, 47, 38, 47, 47, 19, 19, 19, 19] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 199 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524790581 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790581 Building ZINC001524790583 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001524790583 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/936 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001524790583.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524790583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001524790583 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 5, 5, 5, 5, 8, 20, 20, 20, 20, 20, 40, 48, 48, 40, 48, 48, 20, 20, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 20, 20, 20, 40, 40, 48, 48, 40, 48, 48, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 203 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 937) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/937 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/937' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001524790583.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524790583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001524790583 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 7, 7, 8, 8, 8, 8, 8, 8, 8, 11, 17, 17, 17, 17, 17, 31, 45, 45, 45, 45, 45, 17, 17, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 31, 31, 45, 45, 45, 45, 45, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 167 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 938) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/938 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/938' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001524790583.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001524790583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001524790583 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 5, 5, 5, 5, 5, 5, 8, 20, 20, 20, 20, 20, 40, 48, 48, 40, 48, 48, 20, 20, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 20, 20, 20, 40, 40, 48, 48, 40, 48, 48, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 208 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 939) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/939 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/939' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001524790583.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001524790583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001524790583 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 8, 8, 8, 8, 8, 8, 8, 11, 17, 17, 17, 17, 17, 31, 45, 45, 38, 45, 45, 17, 17, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 31, 31, 45, 45, 45, 45, 45, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 192 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524790583 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 Building ZINC001524790583 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001524790583 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 936) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/936: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001524790583.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524790583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001524790583 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 5, 5, 5, 5, 8, 20, 20, 20, 20, 20, 40, 48, 48, 40, 48, 48, 20, 20, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 20, 20, 20, 40, 40, 48, 48, 40, 48, 48, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 203 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 937) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/937: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001524790583.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524790583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001524790583 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 7, 7, 8, 8, 8, 8, 8, 8, 8, 11, 17, 17, 17, 17, 17, 31, 45, 45, 45, 45, 45, 17, 17, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 31, 31, 45, 45, 45, 45, 45, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 167 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 938) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/938: 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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001524790583.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001524790583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001524790583 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 5, 5, 5, 5, 5, 5, 8, 20, 20, 20, 20, 20, 40, 48, 48, 40, 48, 48, 20, 20, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 20, 20, 20, 40, 40, 48, 48, 40, 48, 48, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 208 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 939) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/939: 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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001524790583.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001524790583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001524790583 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 8, 8, 8, 8, 8, 8, 8, 11, 17, 17, 17, 17, 17, 31, 45, 45, 38, 45, 45, 17, 17, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 31, 31, 45, 45, 45, 45, 45, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 192 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524790583 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 Building ZINC001524790583 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001524790583 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 936) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/936: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001524790583.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524790583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001524790583 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 5, 5, 5, 5, 8, 20, 20, 20, 20, 20, 40, 48, 48, 40, 48, 48, 20, 20, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 20, 20, 20, 40, 40, 48, 48, 40, 48, 48, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 203 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 937) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/937: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001524790583.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524790583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001524790583 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 7, 7, 8, 8, 8, 8, 8, 8, 8, 11, 17, 17, 17, 17, 17, 31, 45, 45, 45, 45, 45, 17, 17, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 31, 31, 45, 45, 45, 45, 45, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 167 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 938) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/938: 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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001524790583.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001524790583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001524790583 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 5, 5, 5, 5, 5, 5, 8, 20, 20, 20, 20, 20, 40, 48, 48, 40, 48, 48, 20, 20, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 20, 20, 20, 40, 40, 48, 48, 40, 48, 48, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 208 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 939) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/939: 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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001524790583.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001524790583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001524790583 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 8, 8, 8, 8, 8, 8, 8, 11, 17, 17, 17, 17, 17, 31, 45, 45, 38, 45, 45, 17, 17, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 31, 31, 45, 45, 45, 45, 45, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 192 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524790583 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 Building ZINC001524790583 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001524790583 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 936) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/936: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001524790583.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524790583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001524790583 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 5, 5, 5, 5, 8, 20, 20, 20, 20, 20, 40, 48, 48, 40, 48, 48, 20, 20, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 20, 20, 20, 40, 40, 48, 48, 40, 48, 48, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 203 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 937) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/937: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001524790583.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524790583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001524790583 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 7, 7, 8, 8, 8, 8, 8, 8, 8, 11, 17, 17, 17, 17, 17, 31, 45, 45, 45, 45, 45, 17, 17, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 31, 31, 45, 45, 45, 45, 45, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 167 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 938) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/938: 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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001524790583.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001524790583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001524790583 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 5, 5, 5, 5, 5, 5, 8, 20, 20, 20, 20, 20, 40, 48, 48, 40, 48, 48, 20, 20, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 20, 20, 20, 40, 40, 48, 48, 40, 48, 48, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 208 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 939) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/939: 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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001524790583.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001524790583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001524790583 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H]1[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 8, 8, 8, 8, 8, 8, 8, 11, 17, 17, 17, 17, 17, 31, 45, 45, 38, 45, 45, 17, 17, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 31, 31, 45, 45, 45, 45, 45, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 192 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524790583 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524790583 Building ZINC001524796110 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524796110' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524796110 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524796110 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524796110/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524796110 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/940 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnc(Oc2ccc(F)cc2F)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524796110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524796110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524796110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524796110 none O=C(Nc1ccnc(Oc2ccc(F)cc2F)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', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 1, 12, 1, 1, 1, 1, 15, 1, 1, 15, 1, 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, 3, 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] 0 hydrogens need rotated 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, 30, 49, 49, 30, 49, 49, 49, 49, 8, 1, 1, 1, 3, 3, 3, 3, 3, 2, 8, 8, 49, 49, 49, 8, 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]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524796110 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524796110/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524796110 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 941) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/941 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/941' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnc(Oc2ccc(F)cc2F)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524796110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524796110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524796110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524796110 none O=C(Nc1ccnc(Oc2ccc(F)cc2F)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', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 1, 12, 1, 1, 1, 1, 15, 1, 1, 15, 1, 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, 3, 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] 0 hydrogens need rotated 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, 29, 48, 48, 48, 48, 48, 48, 48, 8, 1, 1, 1, 3, 3, 3, 3, 3, 2, 8, 8, 48, 48, 48, 8, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524796110 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524796110 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524796110/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524796110/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524796110 Building ZINC001524796110 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524796110' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524796110 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524796110 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524796110/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524796110 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 940) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/940: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnc(Oc2ccc(F)cc2F)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524796110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524796110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524796110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524796110 none O=C(Nc1ccnc(Oc2ccc(F)cc2F)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', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 1, 12, 1, 1, 1, 1, 15, 1, 1, 15, 1, 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, 3, 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] 0 hydrogens need rotated 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, 30, 49, 49, 30, 49, 49, 49, 49, 8, 1, 1, 1, 3, 3, 3, 3, 3, 2, 8, 8, 49, 49, 49, 8, 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]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524796110 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524796110/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524796110 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 941) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/941: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnc(Oc2ccc(F)cc2F)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524796110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524796110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524796110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524796110 none O=C(Nc1ccnc(Oc2ccc(F)cc2F)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', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 1, 12, 1, 1, 1, 1, 15, 1, 1, 15, 1, 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, 3, 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] 0 hydrogens need rotated 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, 29, 48, 48, 48, 48, 48, 48, 48, 8, 1, 1, 1, 3, 3, 3, 3, 3, 2, 8, 8, 48, 48, 48, 8, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524796110 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524796110 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524796110/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524796110/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524796110 Building ZINC001524808961 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524808961' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524808961 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524808961 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524808961/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524808961 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/942 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(C)Cc1cn(c2ccccc2)nc1c1cccs1) `ZINC001524808961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524808961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524808961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001524808961 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(C)Cc1cn(c2ccccc2)nc1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 26, 26, 26, 26, 26, 26, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 36, 34, 35, 4, 5, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524808961 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524808961/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524808961 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 943) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/943 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/943' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(C)Cc1cn(c2ccccc2)nc1c1cccs1) `ZINC001524808961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524808961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524808961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001524808961 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(C)Cc1cn(c2ccccc2)nc1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 25, 25, 25, 25, 25, 25, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 36, 34, 35, 4, 5, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524808961 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524808961 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524808961/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524808961/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524808961 Building ZINC001524808961 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524808961' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524808961 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524808961 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524808961/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524808961 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 942) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(C)Cc1cn(c2ccccc2)nc1c1cccs1) `ZINC001524808961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524808961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524808961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001524808961 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N(C)Cc1cn(c2ccccc2)nc1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 26, 26, 26, 26, 26, 26, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 36, 34, 35, 4, 5, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524808961 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524808961/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524808961 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 943) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(C)Cc1cn(c2ccccc2)nc1c1cccs1) `ZINC001524808961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524808961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524808961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001524808961 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N(C)Cc1cn(c2ccccc2)nc1c1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', '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, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 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, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 25, 25, 25, 25, 25, 25, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 8, 9, 10, 36, 34, 35, 4, 5, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524808961 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524808961 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524808961/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524808961/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524808961 Building ZINC001524810208 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524810208' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524810208 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524810208 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524810208/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524810208 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/944 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cc2ccccc2cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001524810208.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524810208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524810208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001524810208 none CCOC(=O)c1cc2ccccc2cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 27, 25, 5, 25, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 37, 37, 37, 37, 37, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524810208 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524810208/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524810208 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 945) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/945 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/945' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cc2ccccc2cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001524810208.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524810208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524810208/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001524810208 none CCOC(=O)c1cc2ccccc2cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 24, 5, 24, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 36, 36, 36, 36, 36, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524810208 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524810208 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524810208/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524810208/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524810208 Building ZINC001524810208 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524810208' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524810208 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524810208 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524810208/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524810208 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 944) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/944: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cc2ccccc2cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001524810208.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524810208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524810208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001524810208 none CCOC(=O)c1cc2ccccc2cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 27, 25, 5, 25, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 37, 37, 37, 37, 37, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524810208 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524810208/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524810208 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 945) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/945: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cc2ccccc2cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001524810208.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524810208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524810208/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001524810208 none CCOC(=O)c1cc2ccccc2cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C 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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 24, 5, 24, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 36, 36, 36, 36, 36, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524810208 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524810208 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524810208/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524810208/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524810208 Building ZINC001524828100 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524828100' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524828100 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524828100 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524828100/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524828100 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/946 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1cccc(Br)c1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524828100.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524828100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524828100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001524828100 none CCN(Cc1cccc(Br)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', 'Br', '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'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 17, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 6, 3, 6, 11, 26, 26, 26, 26, 26, 25, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 11, 11, 26, 26, 26, 26, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 83 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524828100 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524828100/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524828100 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 947) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/947 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/947' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1cccc(Br)c1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524828100.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524828100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524828100/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001524828100 none CCN(Cc1cccc(Br)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', 'Br', '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'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 17, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 6, 3, 6, 11, 26, 26, 26, 26, 26, 25, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 11, 11, 26, 26, 26, 26, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 90 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524828100 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524828100 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524828100/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524828100/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524828100 Building ZINC001524828100 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524828100' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524828100 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524828100 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524828100/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524828100 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 946) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCN(Cc1cccc(Br)c1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524828100.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524828100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524828100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001524828100 none CCN(Cc1cccc(Br)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', 'Br', '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'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 17, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 6, 3, 6, 11, 26, 26, 26, 26, 26, 25, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 11, 11, 26, 26, 26, 26, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 83 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524828100 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524828100/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524828100 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 947) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCN(Cc1cccc(Br)c1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524828100.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524828100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524828100/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001524828100 none CCN(Cc1cccc(Br)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', 'Br', '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'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 17, 1, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 6, 3, 6, 11, 26, 26, 26, 26, 26, 25, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 11, 11, 26, 26, 26, 26, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 90 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524828100 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524828100 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524828100/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524828100/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524828100 Building ZINC001524853622 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524853622' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524853622 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524853622 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524853622/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524853622 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/948 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(CN(Cc2cccc(C)n2)C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)n1) `ZINC001524853622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524853622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524853622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001524853622 none Cc1cccc(CN(Cc2cccc(C)n2)C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.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, 1, 5, 8, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 13, 5, 3, 5, 12, 23, 23, 23, 23, 23, 23, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 13, 13, 12, 12, 23, 23, 23, 23, 23, 23, 3, 1, 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524853622 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524853622/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524853622 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 949) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/949 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/949' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(CN(Cc2cccc(C)n2)C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)n1) `ZINC001524853622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524853622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524853622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001524853622 none Cc1cccc(CN(Cc2cccc(C)n2)C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.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, 1, 5, 8, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 11, 4, 2, 4, 11, 22, 22, 22, 22, 22, 22, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 21, 21, 21, 21, 21, 21, 21, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 3, 1, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524853622 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524853622 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524853622/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524853622/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524853622 Building ZINC001524853622 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524853622' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524853622 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524853622 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524853622/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524853622 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 948) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/948: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(CN(Cc2cccc(C)n2)C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)n1) `ZINC001524853622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524853622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524853622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001524853622 none Cc1cccc(CN(Cc2cccc(C)n2)C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.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, 1, 5, 8, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 13, 5, 3, 5, 12, 23, 23, 23, 23, 23, 23, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 13, 13, 12, 12, 23, 23, 23, 23, 23, 23, 3, 1, 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524853622 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524853622/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524853622 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 949) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/949: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(CN(Cc2cccc(C)n2)C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)n1) `ZINC001524853622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524853622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524853622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001524853622 none Cc1cccc(CN(Cc2cccc(C)n2)C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.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, 1, 5, 8, 5, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 11, 4, 2, 4, 11, 22, 22, 22, 22, 22, 22, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 21, 21, 21, 21, 21, 21, 21, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 3, 1, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524853622 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524853622 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524853622/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524853622/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524853622 Building ZINC001524881347 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524881347' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524881347 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524881347 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524881347/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524881347 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/950 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(F)c(Br)cc1Cl)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524881347.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524881347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524881347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524881347 none O=C(Nc1cc(F)c(Br)cc1Cl)[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', 'Br', 'C.ar', 'C.ar', 'Cl', '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, 15, 1, 17, 1, 1, 16, 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: [7, 1, 7, 7, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 11, 11, 11, 11, 11, 7, 32, 32, 11, 11] 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: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524881347 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524881347/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524881347 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 951) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/951 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/951' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(F)c(Br)cc1Cl)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524881347.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524881347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524881347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524881347 none O=C(Nc1cc(F)c(Br)cc1Cl)[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', 'Br', 'C.ar', 'C.ar', 'Cl', '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, 15, 1, 17, 1, 1, 16, 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: [7, 1, 7, 7, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 11, 11, 11, 11, 11, 7, 32, 32, 11, 11] 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: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524881347 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524881347 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524881347/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524881347/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524881347 Building ZINC001524881347 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524881347' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524881347 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524881347 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524881347/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524881347 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 950) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1cc(F)c(Br)cc1Cl)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524881347.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524881347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524881347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524881347 none O=C(Nc1cc(F)c(Br)cc1Cl)[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', 'Br', 'C.ar', 'C.ar', 'Cl', '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, 15, 1, 17, 1, 1, 16, 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: [7, 1, 7, 7, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 11, 11, 11, 11, 11, 7, 32, 32, 11, 11] 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: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524881347 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524881347/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524881347 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 951) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1cc(F)c(Br)cc1Cl)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001524881347.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524881347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524881347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524881347 none O=C(Nc1cc(F)c(Br)cc1Cl)[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', 'Br', 'C.ar', 'C.ar', 'Cl', '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, 15, 1, 17, 1, 1, 16, 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: [7, 1, 7, 7, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 11, 11, 11, 11, 11, 7, 32, 32, 11, 11] 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: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524881347 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524881347 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524881347/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524881347/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524881347 Building ZINC001524889260 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524889260' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524889260 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524889260 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524889260/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524889260 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/952 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(c2ccc(Br)s2)cs1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001524889260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524889260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524889260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524889260 none O=C(Nc1nc(c2ccc(Br)s2)cs1)[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.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 17, 14, 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] 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, 8, 8, 8, 21, 21, 21, 21, 21, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 21, 21, 8, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524889260 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524889260/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524889260 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 953) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/953 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/953' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(c2ccc(Br)s2)cs1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001524889260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524889260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524889260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524889260 none O=C(Nc1nc(c2ccc(Br)s2)cs1)[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.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 17, 14, 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] 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, 8, 8, 8, 22, 22, 22, 22, 22, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 22, 22, 8, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524889260 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524889260 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524889260/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524889260/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524889260 Building ZINC001524889260 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524889260' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524889260 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524889260 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524889260/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524889260 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 952) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1nc(c2ccc(Br)s2)cs1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001524889260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524889260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524889260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524889260 none O=C(Nc1nc(c2ccc(Br)s2)cs1)[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.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 17, 14, 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] 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, 8, 8, 8, 21, 21, 21, 21, 21, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 21, 21, 8, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524889260 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524889260/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524889260 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 953) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1nc(c2ccc(Br)s2)cs1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001524889260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524889260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524889260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001524889260 none O=C(Nc1nc(c2ccc(Br)s2)cs1)[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.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 17, 14, 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] 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, 8, 8, 8, 22, 22, 22, 22, 22, 8, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 4, 22, 22, 8, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524889260 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524889260 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524889260/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524889260/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524889260 Building ZINC001524900507 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524900507' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524900507 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524900507 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524900507/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524900507 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/954 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1CCCN2C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)c1ccc(F)cc1) `ZINC001524900507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524900507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524900507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001524900507 none O=C(Nc1cccc2c1CCCN2C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)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.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', 'Cl', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 3, 12, 1, 1, 1, 6, 6, 6, 6, 6, 33, 36, 36, 33, 36, 36, 36, 33, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 36, 36, 36, 36] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 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, 45]) total number of confs: 118 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524900507 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524900507/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524900507 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 955) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/955 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/955' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c1CCCN2C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)c1ccc(F)cc1) `ZINC001524900507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524900507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524900507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001524900507 none O=C(Nc1cccc2c1CCCN2C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)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.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', 'Cl', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 3, 12, 1, 1, 1, 5, 5, 5, 5, 5, 33, 35, 35, 33, 33, 35, 35, 33, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 35, 35, 35, 35] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 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, 45]) total number of confs: 105 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524900507 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524900507 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524900507/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524900507/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524900507 Building ZINC001524900507 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524900507' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524900507 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524900507 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524900507/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524900507 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 954) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(Nc1cccc2c1CCCN2C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)c1ccc(F)cc1) `ZINC001524900507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524900507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524900507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001524900507 none O=C(Nc1cccc2c1CCCN2C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)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.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', 'Cl', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 3, 12, 1, 1, 1, 6, 6, 6, 6, 6, 33, 36, 36, 33, 36, 36, 36, 33, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 36, 36, 36, 36] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 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, 45]) total number of confs: 118 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524900507 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524900507/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524900507 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 955) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(Nc1cccc2c1CCCN2C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)c1ccc(F)cc1) `ZINC001524900507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524900507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524900507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001524900507 none O=C(Nc1cccc2c1CCCN2C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)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.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', 'Cl', 'S.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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 3, 12, 1, 1, 1, 5, 5, 5, 5, 5, 33, 35, 35, 33, 33, 35, 35, 33, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 35, 35, 35, 35] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 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, 45]) total number of confs: 105 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524900507 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524900507 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524900507/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524900507/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524900507 Building ZINC001524901067 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524901067' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524901067 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524901067 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524901067/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524901067 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/956 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/956' -> `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)CCOc1ccccc1C(C)(C)C) `ZINC001524901067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524901067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524901067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001524901067 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CCOc1ccccc1C(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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 9, 10, 28, 38, 38, 29, 38, 38, 38, 38, 38, 38, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 4, 4, 4, 9, 9, 10, 10, 38, 38, 31, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 121 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524901067 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524901067/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524901067 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 957) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/957 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/957' -> `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)CCOc1ccccc1C(C)(C)C) `ZINC001524901067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524901067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524901067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001524901067 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CCOc1ccccc1C(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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 9, 10, 27, 37, 37, 37, 37, 37, 37, 37, 37, 37, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 4, 4, 4, 9, 9, 10, 10, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 92 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524901067 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524901067 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524901067/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524901067/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524901067 Building ZINC001524901067 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524901067' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524901067 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524901067 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524901067/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524901067 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 956) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/956: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CCOc1ccccc1C(C)(C)C) `ZINC001524901067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524901067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524901067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001524901067 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CCOc1ccccc1C(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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 9, 10, 28, 38, 38, 29, 38, 38, 38, 38, 38, 38, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 4, 4, 4, 9, 9, 10, 10, 38, 38, 31, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 121 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524901067 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524901067/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524901067 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 957) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/957: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CCOc1ccccc1C(C)(C)C) `ZINC001524901067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524901067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524901067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001524901067 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CCOc1ccccc1C(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', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 9, 10, 27, 37, 37, 37, 37, 37, 37, 37, 37, 37, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 4, 4, 4, 9, 9, 10, 10, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 92 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524901067 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524901067 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524901067/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524901067/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524901067 Building ZINC001524953371 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524953371' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524953371 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524953371 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524953371/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524953371 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/958 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3cc(Cl)cc(Br)c32)cc1Cl) `ZINC001524953371.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524953371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524953371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001524953371 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3cc(Cl)cc(Br)c32)cc1Cl NO_LONG_NAME dock atom 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', 'Cl', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 5, 1, 1, 1, 16, 1, 1, 17, 1, 1, 1, 16, 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] 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: [12, 8, 2, 8, 8, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 12, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 26 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 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: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524953371 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524953371/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524953371 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 959) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/959 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/959' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(Cl)cc(Br)c32)cc1Cl) `ZINC001524953371.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524953371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524953371/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001524953371 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(Cl)cc(Br)c32)cc1Cl NO_LONG_NAME dock atom 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', 'Cl', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 5, 1, 1, 1, 16, 1, 1, 17, 1, 1, 1, 16, 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] 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: [12, 8, 2, 8, 8, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 12, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 28 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 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: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524953371 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524953371 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524953371/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524953371/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524953371 Building ZINC001524953371 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524953371' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524953371 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524953371 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524953371/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524953371 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 958) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3cc(Cl)cc(Br)c32)cc1Cl) `ZINC001524953371.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524953371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524953371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001524953371 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCCc3cc(Cl)cc(Br)c32)cc1Cl NO_LONG_NAME dock atom 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', 'Cl', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 5, 1, 1, 1, 16, 1, 1, 17, 1, 1, 1, 16, 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] 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: [12, 8, 2, 8, 8, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 12, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 26 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 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: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524953371 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524953371/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524953371 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 959) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(Cl)cc(Br)c32)cc1Cl) `ZINC001524953371.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524953371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524953371/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001524953371 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCCc3cc(Cl)cc(Br)c32)cc1Cl NO_LONG_NAME dock atom 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', 'Cl', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 5, 1, 1, 1, 16, 1, 1, 17, 1, 1, 1, 16, 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] 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: [12, 8, 2, 8, 8, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 12, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 28 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 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: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524953371 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524953371 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524953371/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524953371/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524953371 Building ZINC001524967262 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524967262' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524967262 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524967262 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524967262/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524967262 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/960 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(C(=O)N2CCCCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524967262.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524967262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524967262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001524967262 none CCOc1ccc(C(=O)N2CCCCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 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, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 9, 9, 9, 9, 9, 15, 26, 33, 33, 33, 33, 33, 33, 9, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 23, 23, 23, 23, 23, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 9, 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, 51]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524967262 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524967262/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524967262 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 961) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/961 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/961' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(C(=O)N2CCCCC2)cc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524967262.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524967262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524967262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001524967262 none CCOc1ccc(C(=O)N2CCCCC2)cc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 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, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 9, 9, 9, 9, 9, 15, 25, 34, 34, 34, 34, 34, 34, 9, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 22, 22, 22, 22, 22, 9, 9, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 9, 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, 51]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524967262 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524967262 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524967262/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524967262/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524967262 Building ZINC001524967262 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524967262' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524967262 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524967262 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524967262/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524967262 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 960) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOc1ccc(C(=O)N2CCCCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524967262.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524967262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524967262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001524967262 none CCOc1ccc(C(=O)N2CCCCC2)cc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 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, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 9, 9, 9, 9, 9, 15, 26, 33, 33, 33, 33, 33, 33, 9, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 23, 23, 23, 23, 23, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 9, 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, 51]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524967262 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524967262/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524967262 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 961) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCOc1ccc(C(=O)N2CCCCC2)cc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001524967262.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524967262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524967262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001524967262 none CCOc1ccc(C(=O)N2CCCCC2)cc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 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, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 9, 9, 9, 9, 9, 15, 25, 34, 34, 34, 34, 34, 34, 9, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 22, 22, 22, 22, 22, 9, 9, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 9, 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, 51]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524967262 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524967262 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524967262/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524967262/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524967262 Building ZINC001524974535 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524974535' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524974535 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524974535 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524974535/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524974535 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/962 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/962' -> `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)NCCCc1ccccc1F) `ZINC001524974535.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524974535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524974535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001524974535 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCc1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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', '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, 1, 1, 1, 1, 1, 1, 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, 11, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 3, 8, 2, 2, 2, 2, 10, 10, 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]) total number of confs: 108 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524974535 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524974535/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524974535 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 963) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/963 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/963' -> `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)NCCCc1ccccc1F) `ZINC001524974535.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524974535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524974535/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001524974535 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCc1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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', '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, 1, 1, 1, 1, 1, 1, 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, 11, 10, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 11, 11, 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: 101 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524974535 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524974535 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524974535/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524974535/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524974535 Building ZINC001524974535 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524974535' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524974535 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524974535 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524974535/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524974535 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 962) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCc1ccccc1F) `ZINC001524974535.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524974535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524974535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001524974535 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCc1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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', '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, 1, 1, 1, 1, 1, 1, 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, 11, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 3, 8, 2, 2, 2, 2, 10, 10, 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]) total number of confs: 108 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524974535 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524974535/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524974535 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 963) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCc1ccccc1F) `ZINC001524974535.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524974535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524974535/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001524974535 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCc1ccccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', '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', '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, 1, 1, 1, 1, 1, 1, 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, 11, 10, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 11, 11, 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: 101 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524974535 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524974535 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524974535/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524974535/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524974535 Building ZINC001524993306 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524993306' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524993306 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524993306 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524993306/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524993306 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/964 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OCC(F)F)c(C(F)(F)F)c2)cc1Cl) `ZINC001524993306.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524993306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524993306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001524993306 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OCC(F)F)c(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', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 12, 5, 5, 15, 15, 1, 5, 15, 15, 15, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 2, 2, 12, 20, 28, 28, 7, 7, 7, 7, 7, 7, 4, 4, 4, 7, 7, 7, 4, 4, 2, 7, 7, 20, 20, 28, 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: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524993306 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524993306/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524993306 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 965) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/965 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/965' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(OCC(F)F)c(C(F)(F)F)c2)cc1Cl) `ZINC001524993306.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524993306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524993306/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001524993306 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(OCC(F)F)c(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', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 12, 5, 5, 15, 15, 1, 5, 15, 15, 15, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 25, 29, 29, 7, 7, 7, 7, 7, 7, 4, 4, 4, 8, 8, 8, 4, 4, 2, 7, 7, 25, 25, 29, 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: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524993306 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524993306 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524993306/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524993306/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524993306 Building ZINC001524993306 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524993306' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524993306 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001524993306 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524993306/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524993306 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 964) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OCC(F)F)c(C(F)(F)F)c2)cc1Cl) `ZINC001524993306.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001524993306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524993306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001524993306 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OCC(F)F)c(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', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 12, 5, 5, 15, 15, 1, 5, 15, 15, 15, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 2, 2, 12, 20, 28, 28, 7, 7, 7, 7, 7, 7, 4, 4, 4, 7, 7, 7, 4, 4, 2, 7, 7, 20, 20, 28, 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: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524993306 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524993306/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524993306 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 965) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(OCC(F)F)c(C(F)(F)F)c2)cc1Cl) `ZINC001524993306.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001524993306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524993306/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001524993306 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(OCC(F)F)c(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', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 12, 5, 5, 15, 15, 1, 5, 15, 15, 15, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 25, 29, 29, 7, 7, 7, 7, 7, 7, 4, 4, 4, 8, 8, 8, 4, 4, 2, 7, 7, 25, 25, 29, 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: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524993306 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001524993306 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524993306/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524993306/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001524993306 Building ZINC001525005052 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005052' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005052 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525005052 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005052/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005052 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/966 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC[C@H](C)N(Cc1ccc(Br)cc1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001525005052.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525005052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001525005052 none CCCCCC[C@H](C)N(Cc1ccc(Br)cc1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 17, 1, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens 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, 23, 17, 10, 10, 9, 7, 9, 9, 4, 7, 12, 12, 12, 12, 12, 12, 12, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 24, 24, 24, 24, 24, 23, 23, 17, 17, 10, 10, 10, 10, 9, 9, 9, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 5] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005052 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005052/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005052 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 967) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/967 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/967' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC[C@H](C)N(Cc1ccc(Br)cc1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001525005052.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525005052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005052/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001525005052 none CCCCCC[C@H](C)N(Cc1ccc(Br)cc1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 17, 1, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 18, 11, 11, 7, 5, 7, 7, 2, 5, 7, 8, 8, 7, 8, 8, 8, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 28, 28, 28, 28, 28, 28, 28, 18, 18, 11, 11, 11, 11, 7, 7, 7, 7, 7, 8, 8, 8, 8, 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, 54]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005052 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525005052 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005052/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005052/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005052 Building ZINC001525005052 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005052' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005052 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525005052 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005052/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005052 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 966) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCCCCC[C@H](C)N(Cc1ccc(Br)cc1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001525005052.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525005052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001525005052 none CCCCCC[C@H](C)N(Cc1ccc(Br)cc1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 17, 1, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens 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, 23, 17, 10, 10, 9, 7, 9, 9, 4, 7, 12, 12, 12, 12, 12, 12, 12, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 24, 24, 24, 24, 24, 23, 23, 17, 17, 10, 10, 10, 10, 9, 9, 9, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 5] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005052 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005052/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005052 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 967) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCCCCC[C@H](C)N(Cc1ccc(Br)cc1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001525005052.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525005052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005052/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001525005052 none CCCCCC[C@H](C)N(Cc1ccc(Br)cc1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 17, 1, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 18, 11, 11, 7, 5, 7, 7, 2, 5, 7, 8, 8, 7, 8, 8, 8, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 28, 28, 28, 28, 28, 28, 28, 18, 18, 11, 11, 11, 11, 7, 7, 7, 7, 7, 8, 8, 8, 8, 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, 54]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005052 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525005052 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005052/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005052/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005052 Building ZINC001525005053 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005053' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005053 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525005053 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005053/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005053 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/968 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC[C@@H](C)N(Cc1ccc(Br)cc1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001525005053.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525005053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001525005053 none CCCCCC[C@@H](C)N(Cc1ccc(Br)cc1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 17, 1, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 18, 11, 11, 7, 5, 7, 7, 2, 5, 7, 8, 8, 7, 8, 8, 8, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 28, 28, 28, 28, 28, 28, 28, 18, 18, 11, 11, 11, 11, 7, 7, 7, 7, 7, 8, 8, 8, 8, 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, 54]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005053 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005053/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005053 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 969) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/969 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/969' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC[C@@H](C)N(Cc1ccc(Br)cc1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001525005053.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525005053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005053/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001525005053 none CCCCCC[C@@H](C)N(Cc1ccc(Br)cc1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 17, 1, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens 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, 22, 16, 10, 10, 9, 7, 9, 9, 4, 7, 12, 12, 12, 12, 12, 12, 12, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 23, 23, 23, 23, 23, 22, 22, 16, 16, 10, 10, 10, 10, 9, 9, 9, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 5] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005053 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525005053 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005053/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005053/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005053 Building ZINC001525005053 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005053' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005053 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525005053 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005053/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005053 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 968) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCCCCC[C@@H](C)N(Cc1ccc(Br)cc1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001525005053.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525005053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001525005053 none CCCCCC[C@@H](C)N(Cc1ccc(Br)cc1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 17, 1, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 18, 11, 11, 7, 5, 7, 7, 2, 5, 7, 8, 8, 7, 8, 8, 8, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 28, 28, 28, 28, 28, 28, 28, 18, 18, 11, 11, 11, 11, 7, 7, 7, 7, 7, 8, 8, 8, 8, 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, 54]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005053 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005053/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005053 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 969) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCCCCC[C@@H](C)N(Cc1ccc(Br)cc1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001525005053.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525005053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005053/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001525005053 none CCCCCC[C@@H](C)N(Cc1ccc(Br)cc1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 7, 5, 8, 5, 1, 1, 1, 1, 17, 1, 1, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens 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, 22, 16, 10, 10, 9, 7, 9, 9, 4, 7, 12, 12, 12, 12, 12, 12, 12, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 23, 23, 23, 23, 23, 22, 22, 16, 16, 10, 10, 10, 10, 9, 9, 9, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 5] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005053 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525005053 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005053/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005053/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005053 Building ZINC001525005937 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005937' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005937 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525005937 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005937/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005937 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/970 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1) `ZINC001525005937.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525005937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC001525005937 none CN(Cc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', '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', 'Br', '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'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 6, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 45, 45, 45, 45, 45, 45, 45, 45, 45, 25, 25, 6, 6, 6, 6, 2, 4, 4, 45, 45, 45, 45, 45] 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]) total number of confs: 162 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005937 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005937/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005937 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 971) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/971 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/971' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1) `ZINC001525005937.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525005937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005937/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC001525005937 none CN(Cc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', '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', 'Br', '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'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 7, 7, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 48, 26, 26, 7, 7, 7, 7, 2, 4, 4, 48, 48, 48, 48, 48] 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]) total number of confs: 171 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005937 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525005937 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005937/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005937/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005937 Building ZINC001525005937 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005937' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005937 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525005937 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005937/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005937 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 970) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CN(Cc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1) `ZINC001525005937.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525005937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC001525005937 none CN(Cc1ccccc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', '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', 'Br', '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'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 6, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 45, 45, 45, 45, 45, 45, 45, 45, 45, 25, 25, 6, 6, 6, 6, 2, 4, 4, 45, 45, 45, 45, 45] 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]) total number of confs: 162 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005937 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005937/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005937 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 971) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CN(Cc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1) `ZINC001525005937.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525005937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005937/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC001525005937 none CN(Cc1ccccc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', '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', 'Br', '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'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 7, 7, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 48, 48, 48, 48, 48, 48, 48, 48, 48, 26, 26, 7, 7, 7, 7, 2, 4, 4, 48, 48, 48, 48, 48] 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]) total number of confs: 171 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005937 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525005937 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005937/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005937/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525005937 Building ZINC001525032607 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032607' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032607 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525032607 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032607/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032607 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/972 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)c(Cl)c1)[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001525032607.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525032607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001525032607 none O=C(Nc1ccc(Cl)c(Cl)c1)[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', '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, 16, 1, 16, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 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] dock color type numbers: [6, 7, 4, 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: [9, 5, 9, 9, 27, 27, 27, 27, 27, 27, 27, 5, 5, 5, 5, 5, 5, 4, 1, 5, 1, 1, 1, 6, 6, 9, 9, 6, 9, 9, 9, 9, 27, 27, 27, 5, 5, 5, 5, 5, 5, 5, 5, 6, 9, 9, 9, 9, 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]) total number of confs: 80 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032607 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032607/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032607 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 973) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/973 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/973' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)c(Cl)c1)[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001525032607.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525032607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001525032607 none O=C(Nc1ccc(Cl)c(Cl)c1)[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', '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, 16, 1, 16, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 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] dock color type numbers: [6, 7, 4, 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: [8, 5, 8, 8, 25, 25, 25, 25, 25, 25, 25, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 8, 25, 25, 25, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032607 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525032607 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032607/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032607/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032607 Building ZINC001525032607 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032607' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032607 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525032607 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032607/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032607 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 972) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ccc(Cl)c(Cl)c1)[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001525032607.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525032607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001525032607 none O=C(Nc1ccc(Cl)c(Cl)c1)[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', '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, 16, 1, 16, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 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] dock color type numbers: [6, 7, 4, 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: [9, 5, 9, 9, 27, 27, 27, 27, 27, 27, 27, 5, 5, 5, 5, 5, 5, 4, 1, 5, 1, 1, 1, 6, 6, 9, 9, 6, 9, 9, 9, 9, 27, 27, 27, 5, 5, 5, 5, 5, 5, 5, 5, 6, 9, 9, 9, 9, 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]) total number of confs: 80 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032607 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032607/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032607 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 973) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ccc(Cl)c(Cl)c1)[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001525032607.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525032607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001525032607 none O=C(Nc1ccc(Cl)c(Cl)c1)[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', '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, 16, 1, 16, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 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] dock color type numbers: [6, 7, 4, 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: [8, 5, 8, 8, 25, 25, 25, 25, 25, 25, 25, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 8, 25, 25, 25, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032607 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525032607 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032607/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032607/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032607 Building ZINC001525032609 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032609' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032609 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525032609 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032609/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032609 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/974 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)c(Cl)c1)[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001525032609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525032609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001525032609 none O=C(Nc1ccc(Cl)c(Cl)c1)[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', '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, 16, 1, 16, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 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] dock color type numbers: [6, 7, 4, 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: [8, 5, 8, 8, 25, 25, 25, 25, 25, 25, 25, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 8, 25, 25, 25, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032609 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032609/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032609 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 975) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/975 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/975' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)c(Cl)c1)[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001525032609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525032609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001525032609 none O=C(Nc1ccc(Cl)c(Cl)c1)[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', '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, 16, 1, 16, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 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] dock color type numbers: [6, 7, 4, 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: [10, 5, 10, 10, 29, 29, 29, 29, 29, 29, 29, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 10, 29, 29, 29, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032609 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525032609 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032609/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032609/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032609 Building ZINC001525032609 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032609' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032609 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525032609 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032609/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032609 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 974) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ccc(Cl)c(Cl)c1)[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001525032609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525032609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001525032609 none O=C(Nc1ccc(Cl)c(Cl)c1)[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', '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, 16, 1, 16, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 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] dock color type numbers: [6, 7, 4, 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: [8, 5, 8, 8, 25, 25, 25, 25, 25, 25, 25, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 8, 25, 25, 25, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032609 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032609/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032609 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 975) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: O=C(Nc1ccc(Cl)c(Cl)c1)[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001525032609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525032609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001525032609 none O=C(Nc1ccc(Cl)c(Cl)c1)[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', '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, 16, 1, 16, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 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] dock color type numbers: [6, 7, 4, 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: [10, 5, 10, 10, 29, 29, 29, 29, 29, 29, 29, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 10, 29, 29, 29, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032609 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525032609 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032609/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032609/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525032609 Building ZINC001525040595 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525040595' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525040595 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525040595 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525040595/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525040595 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/976 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/976' -> `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)N1CCCc2cc(OC(F)(F)F)ccc21) `ZINC001525040595.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525040595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525040595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001525040595 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCc2cc(OC(F)(F)F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'F', 'F', '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'] 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, 12, 5, 15, 15, 15, 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, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 1, 1, 1, 3, 5, 8, 8, 8, 8, 8, 8, 8, 8, 40, 41, 41, 41, 8, 8, 8, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 77 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525040595 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525040595/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525040595 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 977) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/977 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/977' -> `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)N1CCCc2cc(OC(F)(F)F)ccc21) `ZINC001525040595.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525040595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525040595/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001525040595 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCc2cc(OC(F)(F)F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'F', 'F', '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'] 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, 12, 5, 15, 15, 15, 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, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 4, 7, 7, 3, 3, 1, 1, 1, 3, 5, 8, 8, 8, 8, 8, 8, 8, 8, 40, 40, 40, 40, 8, 8, 8, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 70 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525040595 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525040595 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525040595/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525040595/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525040595 Building ZINC001525040595 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525040595' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525040595 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525040595 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525040595/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525040595 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 976) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCc2cc(OC(F)(F)F)ccc21) `ZINC001525040595.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525040595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525040595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001525040595 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCc2cc(OC(F)(F)F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'F', 'F', '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'] 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, 12, 5, 15, 15, 15, 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, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 1, 1, 1, 3, 5, 8, 8, 8, 8, 8, 8, 8, 8, 40, 41, 41, 41, 8, 8, 8, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 77 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525040595 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525040595/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525040595 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 977) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCc2cc(OC(F)(F)F)ccc21) `ZINC001525040595.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525040595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525040595/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001525040595 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCc2cc(OC(F)(F)F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', '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', 'O.3', 'C.3', 'F', 'F', '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'] 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, 12, 5, 15, 15, 15, 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, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 4, 7, 7, 3, 3, 1, 1, 1, 3, 5, 8, 8, 8, 8, 8, 8, 8, 8, 40, 40, 40, 40, 8, 8, 8, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 70 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525040595 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525040595 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525040595/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525040595/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525040595 Building ZINC001525055295 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525055295' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525055295 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525055295 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525055295/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525055295 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/978 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/978' -> `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)s2)cc1) `ZINC001525055295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525055295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525055295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001525055295 none COc1ccc(c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', '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', '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, 14, 1, 1, 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, 7, 7, 7, 4, 9, 6, 8, 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: [50, 50, 50, 50, 50, 16, 16, 16, 16, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16, 8, 8, 2, 2, 2, 50, 50] 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: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525055295 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525055295/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525055295 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 979) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/979 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/979' -> `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)s2)cc1) `ZINC001525055295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525055295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525055295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001525055295 none COc1ccc(c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', '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', '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, 14, 1, 1, 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, 7, 7, 7, 4, 9, 6, 8, 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: [50, 50, 50, 50, 50, 16, 16, 16, 16, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16, 8, 8, 2, 2, 2, 50, 50] 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: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525055295 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525055295 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525055295/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525055295/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525055295 Building ZINC001525055295 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525055295' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525055295 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525055295 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525055295/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525055295 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 978) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc(c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)s2)cc1) `ZINC001525055295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525055295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525055295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001525055295 none COc1ccc(c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', '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', '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, 14, 1, 1, 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, 7, 7, 7, 4, 9, 6, 8, 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: [50, 50, 50, 50, 50, 16, 16, 16, 16, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16, 8, 8, 2, 2, 2, 50, 50] 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: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525055295 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525055295/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525055295 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 979) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc(c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)s2)cc1) `ZINC001525055295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525055295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525055295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001525055295 none COc1ccc(c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)s2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', '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', '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, 14, 1, 1, 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, 7, 7, 7, 4, 9, 6, 8, 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: [50, 50, 50, 50, 50, 16, 16, 16, 16, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16, 8, 8, 2, 2, 2, 50, 50] 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: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525055295 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525055295 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525055295/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525055295/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525055295 Building ZINC001525056622 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525056622' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525056622 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525056622 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525056622/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525056622 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/980 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(COc2ccc(Br)cc2)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001525056622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525056622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525056622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001525056622 none O=C(Nc1ccc(COc2ccc(Br)cc2)cc1)[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.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 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, 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, 7] 0 hydrogens need 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, 9, 9, 4, 6, 34, 50, 50, 50, 50, 50, 50, 50, 9, 9, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 9, 9, 34, 34, 50, 50, 50, 50, 9, 9, 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]) total number of confs: 174 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525056622 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525056622/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525056622 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 981) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/981 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/981' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(COc2ccc(Br)cc2)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001525056622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525056622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525056622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001525056622 none O=C(Nc1ccc(COc2ccc(Br)cc2)cc1)[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.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 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, 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, 7] 0 hydrogens need 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, 4, 4, 30, 50, 50, 50, 50, 50, 50, 50, 11, 11, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 11, 11, 30, 30, 50, 50, 50, 50, 11, 11, 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]) total number of confs: 165 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525056622 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525056622 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525056622/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525056622/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525056622 Building ZINC001525056622 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525056622' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525056622 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525056622 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525056622/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525056622 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 980) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(Nc1ccc(COc2ccc(Br)cc2)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001525056622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525056622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525056622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001525056622 none O=C(Nc1ccc(COc2ccc(Br)cc2)cc1)[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.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 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, 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, 7] 0 hydrogens need 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, 9, 9, 4, 6, 34, 50, 50, 50, 50, 50, 50, 50, 9, 9, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 9, 9, 34, 34, 50, 50, 50, 50, 9, 9, 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]) total number of confs: 174 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525056622 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525056622/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525056622 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 981) grep: /scratch/xiaobo/12845/xbi-8058088.35/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(Nc1ccc(COc2ccc(Br)cc2)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001525056622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525056622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525056622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001525056622 none O=C(Nc1ccc(COc2ccc(Br)cc2)cc1)[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.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 15, 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, 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, 7] 0 hydrogens need 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, 4, 4, 30, 50, 50, 50, 50, 50, 50, 50, 11, 11, 1, 1, 1, 4, 4, 1, 1, 4, 4, 4, 11, 11, 30, 30, 50, 50, 50, 50, 11, 11, 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]) total number of confs: 165 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525056622 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525056622 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525056622/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525056622/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525056622 Building ZINC001525122989 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525122989' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525122989 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525122989 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525122989/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525122989 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/982 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(OC(F)F)c1) `ZINC001525122989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525122989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525122989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001525122989 none CCCOc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(OC(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 12, 5, 15, 15, 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, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 16, 16, 16, 16, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 16, 16, 17, 19, 19, 16, 50, 50, 50, 50, 50, 47, 47, 16, 16, 9, 9, 2, 2, 1, 2, 19, 16] 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525122989 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525122989/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525122989 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 983) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/983 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/983' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOc1ccc(CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(OC(F)F)c1) `ZINC001525122989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525122989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525122989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001525122989 none CCCOc1ccc(CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(OC(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 12, 5, 15, 15, 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, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 16, 16, 16, 16, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 16, 16, 17, 19, 19, 16, 50, 50, 50, 50, 50, 47, 47, 16, 16, 9, 9, 2, 2, 1, 2, 19, 16] 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525122989 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525122989 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525122989/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525122989/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525122989 Building ZINC001525122989 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525122989' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525122989 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525122989 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525122989/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525122989 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 982) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCCOc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(OC(F)F)c1) `ZINC001525122989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525122989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525122989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001525122989 none CCCOc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(OC(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 12, 5, 15, 15, 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, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 16, 16, 16, 16, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 16, 16, 17, 19, 19, 16, 50, 50, 50, 50, 50, 47, 47, 16, 16, 9, 9, 2, 2, 1, 2, 19, 16] 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525122989 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525122989/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525122989 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 983) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: CCCOc1ccc(CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(OC(F)F)c1) `ZINC001525122989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525122989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525122989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC001525122989 none CCCOc1ccc(CNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)c(OC(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 12, 5, 15, 15, 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, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 16, 16, 16, 16, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 16, 16, 17, 19, 19, 16, 50, 50, 50, 50, 50, 47, 47, 16, 16, 9, 9, 2, 2, 1, 2, 19, 16] 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525122989 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525122989 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525122989/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525122989/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525122989 Building ZINC001525153143 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525153143' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525153143 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525153143 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525153143/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525153143 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/984 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1nc2cc(C(F)(F)F)ccc2n1Cc1ccco1) `ZINC001525153143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525153143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525153143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001525153143 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1nc2cc(C(F)(F)F)ccc2n1Cc1ccco1 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.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 34, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 4, 9, 9, 9, 34, 34, 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]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525153143 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525153143/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525153143 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 985) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/985 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/985' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1nc2cc(C(F)(F)F)ccc2n1Cc1ccco1) `ZINC001525153143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525153143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525153143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001525153143 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1nc2cc(C(F)(F)F)ccc2n1Cc1ccco1 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.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in 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, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 34, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 4, 10, 10, 10, 34, 34, 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]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525153143 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525153143 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525153143/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525153143/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525153143 Building ZINC001525153143 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525153143' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525153143 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525153143 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525153143/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525153143 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 984) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1nc2cc(C(F)(F)F)ccc2n1Cc1ccco1) `ZINC001525153143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525153143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525153143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001525153143 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1nc2cc(C(F)(F)F)ccc2n1Cc1ccco1 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.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 34, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 4, 9, 9, 9, 34, 34, 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]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525153143 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525153143/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525153143 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 985) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1nc2cc(C(F)(F)F)ccc2n1Cc1ccco1) `ZINC001525153143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525153143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525153143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001525153143 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1nc2cc(C(F)(F)F)ccc2n1Cc1ccco1 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.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in 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, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 34, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 4, 10, 10, 10, 34, 34, 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]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525153143 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525153143 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525153143/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525153143/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525153143 Building ZINC001525155815 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525155815' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525155815 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525155815 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525155815/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525155815 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/986 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)ccc2Br)cc1Cl) `ZINC001525155815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525155815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525155815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001525155815 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)ccc2Br)cc1Cl NO_LONG_NAME dock atom 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', 'Br', '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, 1, 17, 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] 0 hydrogens 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, 9, 2, 9, 9, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 8, 14, 14, 14, 9, 9, 9, 17, 17, 17, 9, 9, 4, 14, 8, 14, 9] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525155815 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525155815/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525155815 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 987) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/987 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/987' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)ccc2Br)cc1Cl) `ZINC001525155815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525155815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525155815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001525155815 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)ccc2Br)cc1Cl NO_LONG_NAME dock atom 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', 'Br', '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, 1, 17, 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] 0 hydrogens 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, 9, 2, 9, 9, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 8, 13, 13, 13, 9, 9, 9, 17, 17, 17, 9, 9, 4, 13, 12, 13, 9] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 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: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525155815 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525155815 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525155815/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525155815/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525155815 Building ZINC001525155815 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525155815' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525155815 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525155815 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525155815/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525155815 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 986) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)ccc2Br)cc1Cl) `ZINC001525155815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525155815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525155815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001525155815 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(Br)ccc2Br)cc1Cl NO_LONG_NAME dock atom 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', 'Br', '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, 1, 17, 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] 0 hydrogens 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, 9, 2, 9, 9, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 8, 14, 14, 14, 9, 9, 9, 17, 17, 17, 9, 9, 4, 14, 8, 14, 9] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525155815 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525155815/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525155815 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 987) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)ccc2Br)cc1Cl) `ZINC001525155815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525155815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525155815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001525155815 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(Br)ccc2Br)cc1Cl NO_LONG_NAME dock atom 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', 'Br', '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, 1, 17, 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] 0 hydrogens 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, 9, 2, 9, 9, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 8, 13, 13, 13, 9, 9, 9, 17, 17, 17, 9, 9, 4, 13, 12, 13, 9] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 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: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525155815 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525155815 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525155815/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525155815/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525155815 Building ZINC001525164388 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525164388' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525164388 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525164388 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525164388/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525164388 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/988 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccc(F)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001525164388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525164388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525164388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001525164388 none CC(C)(C)OC(=O)Nc1ccc(F)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 43, 43, 37, 29, 37, 6, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 6, 43, 43, 43, 43, 43, 43, 43, 43, 43, 29, 6, 6, 3, 5, 5, 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525164388 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525164388/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525164388 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 989) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/989 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/989' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccc(F)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001525164388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525164388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525164388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001525164388 none CC(C)(C)OC(=O)Nc1ccc(F)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 30, 38, 6, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 6, 42, 42, 42, 42, 42, 42, 42, 42, 42, 30, 6, 6, 3, 5, 5, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525164388 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525164388 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525164388/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525164388/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525164388 Building ZINC001525164388 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525164388' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525164388 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525164388 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525164388/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525164388 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 988) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/988: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccc(F)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001525164388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525164388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525164388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001525164388 none CC(C)(C)OC(=O)Nc1ccc(F)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 43, 43, 37, 29, 37, 6, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 6, 43, 43, 43, 43, 43, 43, 43, 43, 43, 29, 6, 6, 3, 5, 5, 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525164388 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525164388/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525164388 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 989) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/989: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccc(F)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001525164388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525164388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525164388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001525164388 none CC(C)(C)OC(=O)Nc1ccc(F)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 30, 38, 6, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 6, 42, 42, 42, 42, 42, 42, 42, 42, 42, 30, 6, 6, 3, 5, 5, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525164388 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525164388 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525164388/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525164388/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525164388 Building ZINC001525240499 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001525240499 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/990 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl) `ZINC001525240499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525240499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001525240499 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 5, 15, 15, 15, 15, 15, 15, 26, 26, 17, 26, 26, 26, 26, 15, 4, 4, 4, 9, 9, 9, 4, 4, 3, 15, 15, 15, 15, 15, 15, 26, 26, 26, 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, 44, 45, 46]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 991) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/991 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/991' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl) `ZINC001525240499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525240499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001525240499 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 14, 25, 25, 25, 25, 25, 25, 25, 14, 4, 4, 4, 9, 9, 9, 4, 4, 2, 14, 14, 14, 14, 14, 14, 25, 25, 25, 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, 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/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 992) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/992 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/992' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl) `ZINC001525240499.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001525240499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001525240499 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 5, 15, 15, 15, 15, 15, 15, 26, 26, 17, 26, 26, 26, 26, 15, 4, 4, 4, 9, 9, 9, 4, 4, 3, 15, 15, 15, 15, 15, 15, 26, 26, 26, 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, 44, 45, 46]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 993) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/993 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/993' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl) `ZINC001525240499.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001525240499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001525240499 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 14, 25, 25, 25, 25, 25, 25, 25, 14, 4, 4, 4, 9, 9, 9, 4, 4, 2, 14, 14, 14, 14, 14, 14, 25, 25, 25, 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, 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/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525240499 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499 Building ZINC001525240499 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001525240499 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 990) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl) `ZINC001525240499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525240499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001525240499 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 5, 15, 15, 15, 15, 15, 15, 26, 26, 17, 26, 26, 26, 26, 15, 4, 4, 4, 9, 9, 9, 4, 4, 3, 15, 15, 15, 15, 15, 15, 26, 26, 26, 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, 44, 45, 46]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 991) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl) `ZINC001525240499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525240499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001525240499 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 14, 25, 25, 25, 25, 25, 25, 25, 14, 4, 4, 4, 9, 9, 9, 4, 4, 2, 14, 14, 14, 14, 14, 14, 25, 25, 25, 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, 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/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 992) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/992: 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]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl) `ZINC001525240499.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001525240499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001525240499 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 5, 15, 15, 15, 15, 15, 15, 26, 26, 17, 26, 26, 26, 26, 15, 4, 4, 4, 9, 9, 9, 4, 4, 3, 15, 15, 15, 15, 15, 15, 26, 26, 26, 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, 44, 45, 46]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 993) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/993: 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]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl) `ZINC001525240499.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001525240499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001525240499 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 14, 25, 25, 25, 25, 25, 25, 25, 14, 4, 4, 4, 9, 9, 9, 4, 4, 2, 14, 14, 14, 14, 14, 14, 25, 25, 25, 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, 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/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525240499 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499 Building ZINC001525240499 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001525240499 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 990) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl) `ZINC001525240499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525240499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001525240499 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 5, 15, 15, 15, 15, 15, 15, 26, 26, 17, 26, 26, 26, 26, 15, 4, 4, 4, 9, 9, 9, 4, 4, 3, 15, 15, 15, 15, 15, 15, 26, 26, 26, 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, 44, 45, 46]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 991) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl) `ZINC001525240499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525240499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001525240499 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 14, 25, 25, 25, 25, 25, 25, 25, 14, 4, 4, 4, 9, 9, 9, 4, 4, 2, 14, 14, 14, 14, 14, 14, 25, 25, 25, 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, 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/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 992) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/992: 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]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl) `ZINC001525240499.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001525240499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001525240499 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 5, 15, 15, 15, 15, 15, 15, 26, 26, 17, 26, 26, 26, 26, 15, 4, 4, 4, 9, 9, 9, 4, 4, 3, 15, 15, 15, 15, 15, 15, 26, 26, 26, 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, 44, 45, 46]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 993) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/993: 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]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl) `ZINC001525240499.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001525240499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001525240499 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 14, 25, 25, 25, 25, 25, 25, 25, 14, 4, 4, 4, 9, 9, 9, 4, 4, 2, 14, 14, 14, 14, 14, 14, 25, 25, 25, 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, 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/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525240499 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499 Building ZINC001525240499 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001525240499 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 990) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl) `ZINC001525240499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525240499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001525240499 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 5, 15, 15, 15, 15, 15, 15, 26, 26, 17, 26, 26, 26, 26, 15, 4, 4, 4, 9, 9, 9, 4, 4, 3, 15, 15, 15, 15, 15, 15, 26, 26, 26, 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, 44, 45, 46]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 991) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl) `ZINC001525240499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525240499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001525240499 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 14, 25, 25, 25, 25, 25, 25, 25, 14, 4, 4, 4, 9, 9, 9, 4, 4, 2, 14, 14, 14, 14, 14, 14, 25, 25, 25, 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, 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/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 992) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/992: 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]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl) `ZINC001525240499.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001525240499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001525240499 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 5, 15, 15, 15, 15, 15, 15, 26, 26, 17, 26, 26, 26, 26, 15, 4, 4, 4, 9, 9, 9, 4, 4, 3, 15, 15, 15, 15, 15, 15, 26, 26, 26, 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, 44, 45, 46]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 993) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/993: 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]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl) `ZINC001525240499.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001525240499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001525240499 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 14, 25, 25, 25, 25, 25, 25, 25, 14, 4, 4, 4, 9, 9, 9, 4, 4, 2, 14, 14, 14, 14, 14, 14, 25, 25, 25, 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, 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/12845/xbi-8058088.35/working/building/ZINC001525240499 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525240499 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240499 Building ZINC001525240501 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001525240501 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/994 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl) `ZINC001525240501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525240501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001525240501 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 5, 16, 16, 16, 16, 16, 16, 25, 25, 19, 23, 25, 25, 25, 16, 4, 4, 4, 9, 9, 9, 4, 4, 2, 16, 16, 16, 16, 16, 16, 25, 25, 25, 16, 16, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 995) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/995 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/995' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl) `ZINC001525240501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525240501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001525240501 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 6, 18, 18, 18, 18, 18, 18, 28, 28, 20, 28, 28, 28, 28, 18, 4, 4, 4, 8, 8, 8, 4, 4, 3, 18, 18, 18, 18, 18, 18, 28, 28, 28, 18, 18, 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: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 996) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/996 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/996' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl) `ZINC001525240501.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001525240501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001525240501 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 5, 16, 16, 16, 16, 16, 16, 25, 25, 19, 23, 25, 25, 25, 16, 4, 4, 4, 9, 9, 9, 4, 4, 2, 16, 16, 16, 16, 16, 16, 25, 25, 25, 16, 16, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 997) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/997 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/997' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl) `ZINC001525240501.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001525240501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001525240501 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 6, 18, 18, 18, 18, 18, 18, 28, 28, 20, 28, 28, 28, 28, 18, 4, 4, 4, 8, 8, 8, 4, 4, 3, 18, 18, 18, 18, 18, 18, 28, 28, 28, 18, 18, 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: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525240501 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 Building ZINC001525240501 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001525240501 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 994) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl) `ZINC001525240501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525240501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001525240501 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 5, 16, 16, 16, 16, 16, 16, 25, 25, 19, 23, 25, 25, 25, 16, 4, 4, 4, 9, 9, 9, 4, 4, 2, 16, 16, 16, 16, 16, 16, 25, 25, 25, 16, 16, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 995) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl) `ZINC001525240501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525240501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001525240501 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 6, 18, 18, 18, 18, 18, 18, 28, 28, 20, 28, 28, 28, 28, 18, 4, 4, 4, 8, 8, 8, 4, 4, 3, 18, 18, 18, 18, 18, 18, 28, 28, 28, 18, 18, 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: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 996) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/996: 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]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl) `ZINC001525240501.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001525240501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001525240501 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 5, 16, 16, 16, 16, 16, 16, 25, 25, 19, 23, 25, 25, 25, 16, 4, 4, 4, 9, 9, 9, 4, 4, 2, 16, 16, 16, 16, 16, 16, 25, 25, 25, 16, 16, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 997) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/997: 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]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl) `ZINC001525240501.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001525240501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001525240501 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 6, 18, 18, 18, 18, 18, 18, 28, 28, 20, 28, 28, 28, 28, 18, 4, 4, 4, 8, 8, 8, 4, 4, 3, 18, 18, 18, 18, 18, 18, 28, 28, 28, 18, 18, 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: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525240501 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 Building ZINC001525240501 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001525240501 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 994) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl) `ZINC001525240501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525240501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001525240501 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 5, 16, 16, 16, 16, 16, 16, 25, 25, 19, 23, 25, 25, 25, 16, 4, 4, 4, 9, 9, 9, 4, 4, 2, 16, 16, 16, 16, 16, 16, 25, 25, 25, 16, 16, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 995) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl) `ZINC001525240501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525240501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001525240501 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 6, 18, 18, 18, 18, 18, 18, 28, 28, 20, 28, 28, 28, 28, 18, 4, 4, 4, 8, 8, 8, 4, 4, 3, 18, 18, 18, 18, 18, 18, 28, 28, 28, 18, 18, 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: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 996) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/996: 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]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl) `ZINC001525240501.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001525240501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001525240501 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 5, 16, 16, 16, 16, 16, 16, 25, 25, 19, 23, 25, 25, 25, 16, 4, 4, 4, 9, 9, 9, 4, 4, 2, 16, 16, 16, 16, 16, 16, 25, 25, 25, 16, 16, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 997) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/997: 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]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl) `ZINC001525240501.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001525240501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001525240501 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 6, 18, 18, 18, 18, 18, 18, 28, 28, 20, 28, 28, 28, 28, 18, 4, 4, 4, 8, 8, 8, 4, 4, 3, 18, 18, 18, 18, 18, 18, 28, 28, 28, 18, 18, 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: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525240501 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 Building ZINC001525240501 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001525240501 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 994) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl) `ZINC001525240501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525240501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001525240501 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 5, 16, 16, 16, 16, 16, 16, 25, 25, 19, 23, 25, 25, 25, 16, 4, 4, 4, 9, 9, 9, 4, 4, 2, 16, 16, 16, 16, 16, 16, 25, 25, 25, 16, 16, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 995) grep: /scratch/xiaobo/12845/xbi-8058088.35/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl) `ZINC001525240501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525240501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001525240501 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 6, 18, 18, 18, 18, 18, 18, 28, 28, 20, 28, 28, 28, 28, 18, 4, 4, 4, 8, 8, 8, 4, 4, 3, 18, 18, 18, 18, 18, 18, 28, 28, 28, 18, 18, 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: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `2' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/2 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 2 (index: 996) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/996: 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]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl) `ZINC001525240501.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001525240501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001525240501 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 5, 16, 16, 16, 16, 16, 16, 25, 25, 19, 23, 25, 25, 25, 16, 4, 4, 4, 9, 9, 9, 4, 4, 2, 16, 16, 16, 16, 16, 16, 25, 25, 25, 16, 16, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `3' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/3 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 3 (index: 997) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/997: 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]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl) `ZINC001525240501.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001525240501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001525240501 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3ccc(Cl)cc3Cl)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 6, 18, 18, 18, 18, 18, 18, 28, 28, 20, 28, 28, 28, 28, 18, 4, 4, 4, 8, 8, 8, 4, 4, 3, 18, 18, 18, 18, 18, 18, 28, 28, 28, 18, 18, 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: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525240501 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 3: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/3.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/0.* 2: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501/2.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525240501 Building ZINC001525254945 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525254945' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525254945 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525254945 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525254945/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525254945 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/998 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/998' -> `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(CCC(=O)OC(C)(C)C)c1) `ZINC001525254945.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525254945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525254945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001525254945 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(CCC(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 2, 5, 5, 9, 12, 50, 50, 50, 50, 50, 50, 5, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 5, 5, 2, 9, 9, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525254945 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525254945/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525254945 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 999) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/999 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/999' -> `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(CCC(=O)OC(C)(C)C)c1) `ZINC001525254945.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525254945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525254945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001525254945 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(CCC(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 4, 4, 8, 10, 50, 50, 50, 50, 50, 50, 4, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 4, 4, 4, 8, 8, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525254945 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525254945 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525254945/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525254945/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525254945 Building ZINC001525254945 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525254945' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525254945 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525254945 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525254945/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525254945 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 998) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/998: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(CCC(=O)OC(C)(C)C)c1) `ZINC001525254945.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525254945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525254945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001525254945 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(CCC(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 2, 5, 5, 9, 12, 50, 50, 50, 50, 50, 50, 5, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 5, 5, 2, 9, 9, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525254945 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 mkdir: created directory `1' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525254945/1 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525254945 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 1 (index: 999) grep: /scratch/xiaobo/12845/xbi-8058088.35/working/3D/999: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(CCC(=O)OC(C)(C)C)c1) `ZINC001525254945.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525254945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525254945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001525254945 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(CCC(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 4, 4, 8, 10, 50, 50, 50, 50, 50, 50, 4, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 4, 4, 4, 8, 8, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525254945 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525254945 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 1: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525254945/1.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525254945/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525254945 Building ZINC001525309064 mkdir: created directory `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525309064' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525309064 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC001525309064 mkdir: created directory `0' /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525309064/0 /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525309064 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/xiaobo/12845/xbi-8058088.35/working/3D/1000 `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cnn1c1ccc(Cl)cc1) `ZINC001525309064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525309064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525309064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001525309064 none CCc1c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cnn1c1ccc(Cl)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', 'Br', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 8, 8, 1, 1, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 9, 9, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 20, 20, 20, 20, 20, 20, 18, 18, 18, 18, 18, 5, 9, 9, 9, 20, 20, 20, 20] 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: 100 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525309064 /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Finished preparing ZINC001525309064 Recording results /scratch/xiaobo/12845/xbi-8058088.35/working /scratch/xiaobo/12845/xbi-8058088.35 Appending to /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.* 0: /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525309064/0.* Removing working files in /scratch/xiaobo/12845/xbi-8058088.35/working/building/ZINC001525309064 /scratch/xiaobo/12845/xbi-8058088.35 Compressing combined databse files /scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.db2.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/xiaobo/12845/xbi-8058088.35/finished) ======================================================= Finalizing... removed `/scratch/xiaobo/12845/xbi-8058088.35/working/3D/1001' removed directory: `/scratch/xiaobo/12845/xbi-8058088.35/working/3D' `/scratch/xiaobo/12845/xbi-8058088.35/working/protonate' -> `/scratch/xiaobo/12845/xbi-8058088.35/archive' `/scratch/xiaobo/12845/xbi-8058088.35/working/input-smiles.ism' -> `/scratch/xiaobo/12845/xbi-8058088.35/archive/input-smiles.ism' rmdir: removing directory, `/scratch/xiaobo/12845/xbi-8058088.35/working/building' rmdir: removing directory, `/scratch/xiaobo/12845/xbi-8058088.35/working' /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/logs `/scratch/xiaobo/12845/xbi-8058088.35' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi' `/scratch/xiaobo/12845/xbi-8058088.35/finished' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/finished' `/scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/finished/xbi.db2.gz' `/scratch/xiaobo/12845/xbi-8058088.35/failed' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/input.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/input.ism' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878.ism' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/failure-reason' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/failure-reason' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/0' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/0' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/0/0.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/0/0.db2.gz' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/0/temp.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/0/temp.mol2' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/0/fort.12' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/0/fort.12' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/0/outputwat.log' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/0/outputwat.log' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/0/fort.21' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/0/fort.21' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/0/temp.ZmatMOPAC' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/0/temp.ZmatMOPAC' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/0/0.mol2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/0/0.mol2.gz' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/0/output.solv' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/0/output.solv' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/0/fort.20' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/0/fort.20' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/0/temp-working.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/0/temp-working.mol2' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/0/output.1.db2in.mol2.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/0/output.1.db2in.mol2.db2.gz' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/0/fort.19' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/0/fort.19' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/0/output.1.db2in.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/0/output.1.db2in.mol2' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/0/temp.in-wat' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/0/temp.in-wat' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/0/ZINC001517646878.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/0/ZINC001517646878.mol2' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/0/0.mol2.original' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/0/0.mol2.original' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/0/0.solv' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/0/0.solv' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/0/temp.in-hex' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/0/temp.in-hex' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/0/temp.o-hex' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/0/temp.o-hex' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/0/temp.o-wat' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/0/temp.o-wat' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/0/outputhex.log' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/0/outputhex.log' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/0/output.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/0/output.mol2' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/0/name.txt' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/0/name.txt' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/1.failed' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/1.failed' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/1.failed/temp.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/1.failed/temp.mol2' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/1.failed/fort.12' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/1.failed/fort.12' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/1.failed/outputwat.log' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/1.failed/outputwat.log' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/1.failed/fort.21' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/1.failed/fort.21' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/1.failed/temp.ZmatMOPAC' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/1.failed/temp.ZmatMOPAC' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/1.failed/failure-reason' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/1.failed/failure-reason' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/1.failed/fort.20' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/1.failed/fort.20' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/1.failed/fort.19' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/1.failed/fort.19' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/1.failed/temp.in-wat' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/1.failed/temp.in-wat' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/1.failed/ZINC001517646878.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/1.failed/ZINC001517646878.mol2' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/1.failed/temp.in-hex' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/1.failed/temp.in-hex' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/1.failed/temp.o-hex' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/1.failed/temp.o-hex' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/1.failed/1.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/1.failed/1.mol2' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/1.failed/temp.o-wat' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/1.failed/temp.o-wat' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/1.failed/outputhex.log' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/1.failed/outputhex.log' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/1.failed/name.txt' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/1.failed/name.txt' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/input.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/input.ism' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/ZINC001517646878.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/ZINC001517646878.ism' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/failure-reason' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/failure-reason' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/0' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/0.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/0/0.db2.gz' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/temp.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/0/temp.mol2' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/fort.12' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/0/fort.12' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/outputwat.log' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/0/outputwat.log' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/fort.21' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/0/fort.21' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/temp.ZmatMOPAC' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/0/temp.ZmatMOPAC' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/0.mol2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/0/0.mol2.gz' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/output.solv' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/0/output.solv' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/fort.20' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/0/fort.20' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/temp-working.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/0/temp-working.mol2' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/output.1.db2in.mol2.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/0/output.1.db2in.mol2.db2.gz' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/fort.19' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/0/fort.19' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/output.1.db2in.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/0/output.1.db2in.mol2' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/temp.in-wat' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/0/temp.in-wat' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/ZINC001517646878.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/0/ZINC001517646878.mol2' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/0.mol2.original' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/0/0.mol2.original' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/0.solv' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/0/0.solv' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/temp.in-hex' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/0/temp.in-hex' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/temp.o-hex' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/0/temp.o-hex' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/temp.o-wat' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/0/temp.o-wat' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/outputhex.log' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/0/outputhex.log' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/output.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/0/output.mol2' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/name.txt' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/0/name.txt' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/1.failed' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/1.failed' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/1.failed/temp.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/1.failed/temp.mol2' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/1.failed/fort.12' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/1.failed/fort.12' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/1.failed/outputwat.log' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/1.failed/outputwat.log' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/1.failed/fort.21' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/1.failed/fort.21' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/1.failed/temp.ZmatMOPAC' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/1.failed/temp.ZmatMOPAC' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/1.failed/failure-reason' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/1.failed/failure-reason' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/1.failed/fort.20' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/1.failed/fort.20' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/1.failed/fort.19' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/1.failed/fort.19' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/1.failed/temp.in-wat' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/1.failed/temp.in-wat' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/1.failed/ZINC001517646878.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/1.failed/ZINC001517646878.mol2' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/1.failed/temp.in-hex' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/1.failed/temp.in-hex' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/1.failed/temp.o-hex' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/1.failed/temp.o-hex' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/1.failed/1.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/1.failed/1.mol2' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/1.failed/temp.o-wat' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/1.failed/temp.o-wat' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/1.failed/outputhex.log' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/1.failed/outputhex.log' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/1.failed/name.txt' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/1.failed/name.txt' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/ZINC001517646878-numbered.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/ZINC001517646878-numbered.ism' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/ZINC001517646878.solv' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878/ZINC001517646878.solv' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878-numbered.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878-numbered.ism' `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878.solv' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/failed/ZINC001517646878/ZINC001517646878.solv' `/scratch/xiaobo/12845/xbi-8058088.35/archive' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/archive' `/scratch/xiaobo/12845/xbi-8058088.35/archive/xbi-protomers.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/archive/xbi-protomers.ism' `/scratch/xiaobo/12845/xbi-8058088.35/archive/xbi-protomers-expanded.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/archive/xbi-protomers-expanded.ism' `/scratch/xiaobo/12845/xbi-8058088.35/archive/xbi-protonated-manual.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/archive/xbi-protonated-manual.ism' `/scratch/xiaobo/12845/xbi-8058088.35/archive/input-smiles.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xbi/archive/input-smiles.ism' removed `/scratch/xiaobo/12845/xbi-8058088.35/finished/xbi.db2.gz' removed directory: `/scratch/xiaobo/12845/xbi-8058088.35/finished' removed `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/input.ism' 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`/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/0/outputhex.log' removed `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/0/output.mol2' removed `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/0/name.txt' removed directory: `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/0' removed `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/1.failed/temp.mol2' removed `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/1.failed/fort.12' removed `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/1.failed/outputwat.log' removed `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/1.failed/fort.21' removed `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/1.failed/temp.ZmatMOPAC' removed `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/1.failed/failure-reason' removed `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/1.failed/fort.20' removed 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`/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/input.ism' removed `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/ZINC001517646878.ism' removed `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/failure-reason' removed `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/0.db2.gz' removed `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/temp.mol2' removed `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/fort.12' removed `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/outputwat.log' removed `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/fort.21' removed `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/temp.ZmatMOPAC' removed `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/0.mol2.gz' removed `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/output.solv' removed `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/fort.20' removed `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/temp-working.mol2' removed `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/output.1.db2in.mol2.db2.gz' removed `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/fort.19' removed `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/output.1.db2in.mol2' removed `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/temp.in-wat' removed `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/0/ZINC001517646878.mol2' removed 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`/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878/ZINC001517646878.solv' removed directory: `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878' removed `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878-numbered.ism' removed `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878/ZINC001517646878.solv' removed directory: `/scratch/xiaobo/12845/xbi-8058088.35/failed/ZINC001517646878' removed directory: `/scratch/xiaobo/12845/xbi-8058088.35/failed' removed `/scratch/xiaobo/12845/xbi-8058088.35/archive/xbi-protomers.ism' removed `/scratch/xiaobo/12845/xbi-8058088.35/archive/xbi-protomers-expanded.ism' removed `/scratch/xiaobo/12845/xbi-8058088.35/archive/xbi-protonated-manual.ism' removed `/scratch/xiaobo/12845/xbi-8058088.35/archive/input-smiles.ism' removed directory: `/scratch/xiaobo/12845/xbi-8058088.35/archive' removed directory: `/scratch/xiaobo/12845/xbi-8058088.35'